Questions in topology
 As the study of the properties of spaces that undergo continuous deformations, topology is a major branch of mathematics born from geometry. Examine the foundations of relations, maps, orders, and sets. Explore basic topology on Euclidian space $\mathbb{R}^n$, the set properties of closure and compactness, and how functions are continuous between two topological spaces. Topological spaces are mathematical spaces defined by a set of specific axioms relating points and neighborhoods. Discover how to define and compare topological spaces and explore the concepts of metric and normed spaces. Follow up with a more in depth examination of both open and closed sets, and the associated properties of closure, interior, boundary, and denseness. Continuity of topological spaces is analogous to classical limits. Explore how sequences in topology display convergence and how this leads to a definition of continuity. Apply this to homeomorphisms, continuous functions between topological spaces whose inverses are also continuous. Compactness of topological spaces is akin to finiteness of regular functions and gives spaces a quality of being well-behaved. Determine first how to define compact spaces and, more specifically, sequential compactness. Explore subspaces and define relative and local compactness. Quotient and product spaces focus on creating new topological spaces from others. Learn how to "glue" points of a topological space together to create quotient spaces and how cartesian products of topological spaces can create product spaces. Apply properties of compactness to quotient and product spaces using Tychonoff's Theorem. Separation axioms are a series of restrictions that can be places on topological spaces to help classify different spaces. Learn about the $T_n$ axioms from least to most restrictive and how they apply to regular spaces. A function space is a set of functions between two sets. Explore what it means for a sequence of functions to converge to another function and utilize the Arzela-Ascoli Theorem to determine convergence. Apply compact open topology to function maps between two topological spaces. The fundamental group is a mathematical group that determines if two paths with shared end points can be continuously deformed into each other, also known as homotopy of functions. Define and apply the fundamental group and discover how homomorphisms are induced. The Seifert-van Kampen Theorem allows for the analysis of the fundamental group of spaces that are constructed from simpler ones. Construct new groups from other groups using the free product and apply the Seifert-van Kampen Theorem. Explore basic 2D cell complexes. Covering maps, as applied to homotopy groups, are continuous functions between two topological spaces in which each point from one "covers" or is "covered" by a point in the other, essentially a local homomorphism. Define and construct covering spaces, classify them, and learn to apply deck transformations.
Rafiq Bodalal How to link MATLAB with ANSYS Workbench? I'm currently working on a research project that involves the topology optimization of mechanical components and would like to use metaheuristics to update problem design variables in MATLAB and perform the FEA analysis in ANSYS. I know that the linking of these two software packages are possible, as I have read many papers that employ such methods. I'd appreciate it if researchers can provide a detailed explanation of how to link them together. Stéphane Breton Does the concept of spin-induced recto-verso (i.e. double-sheet) make sense, topologically speaking, in quantum mechanics? A physics experiment [1], driven on an expanding spin-orbit coupled Bose-Einstein condensate, suggested that a self-trapping effect band (explained in terms of the Peierls-Nabarro energy barrier) separates two dispersion domains characterized by a positive mass but a spin reversal. The self-trapping phenomenon was naturally explained by a negative effective mass related to a negative curvature of the underlying dispersion relation (as opposed to parabolic curvatures). To better contextualise my question from a practical point of view, I will quote Wipedia ( follow https://en.wikipedia.org/wiki/Spin_(physics) ): “Mathematically, quantum-mechanical spin states are described by ‘vector-like objects’ known as spinors. There are subtle differences between the behavior of spinors and vectors under coordinate rotations. For example, rotating a spin-1/2 particle by 360° does not bring it back to the same quantum state, but to the state with the opposite quantum phase; this is detectable, in principle, with interference experiments. To return the particle to its exact original state, one needs a 720° rotation (The Plate trick and Möbius strip give non-quantum analogies).” I appeal here to physicists in a spirit of free and friendly discussion. Rakesh Davella Fatal error: Residue 728 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom CA used in that ent? Fatal error: Residue 728 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom CA used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Rey Segundo Guerrero-Proenza Do you know any topological approach to similarity functions in Case Based Reasoning? Defining similarity function or relation in Case Based Reasoning is a key moment for a good result. Frequently numeric functions are used, which is, in fact , an assumption of existing some kind of metric, being cases points of the corresponding space. But what about defining "proximity" of given cases in terms of topological relations? I have being searching but, up to now, I have not found any general approach. Have you any information on this regard? Parmida Rasouli What is the best mesh size and type for topology optimization? Can we use Adaptive-remeshing before topology optimization? Is it advised to use Adaptive-remeshing before topology optimization process? (because sensitive sections on my part (which gain the smallest size of the mesh), are actually frozen in the topology optimization process, and on the other hand, sections that should be removed from topology, have larger mesh and will make coarser surface at the end of the process) Varun Varun Every totally bounded metric space is locally compact ??? I am aware of the facts that every totally bounded metric space is separable and a metric space is compact iff it is totally bounded and complete but I wanted to know, is every totally bounded metric space is locally compact or not. If not, then give an example of a metric space that is totally bounded but not locally compact. Follow this question on the given link https://math.stackexchange.com/questions/4371151/every-totally-bounded-metric-space-is-locally-compact Haidi Said When I create my own topology by the Gui in ifogsim it can not be executed ( the simulation doesn't run ) what's the solution to this problem? Ifogsim topology execution Rajeshkumar K. C. Fungal Phylogeny; Dealing with datasets for a robust phylogeny? Dear Colleagues, I need some advice to resolve the issues associated with building robust phylogeny trees in different fungal families. It is indeed a basic query but may be helpful to many budding mycologists from India and across the globe. We are using graphic version of RAxML and MrBayes for making trees. Unfortunately, we are regularly facing issues related to data deficiency in several fungal families ( It cannot be resolve until sampling and epitypification!!!). But even after retrieval of data based on some published papers; The BS/BYPP values seem to vary considerably from the high values mentioned in the article to a moderate value in our analyses. What are the best practices to deal with it? We choose type strain to build a backbone to assess the topological congruence for different genes too. How best we must edit our datasets to achieve high BS values? How best we can define gaps in RAxML? What are the other parameters taken into account other than model tests? Thanks in advance. Muzher Saleem How to compair topological indices graphically by using mathematics. Give any code? For writing research articles Krithika Unmesh I encountered a fatal error during simulation of ATP using NAMD and VMD. Could anyone please help me rectify ? I was performing the equilibration and minimization of ATP in namd and vmd. This is the error message. FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE top_all27_na.rtf LINE=** \\\\ CHARMM27 All-Hydrogen Nucleic Acid Topology File ////* Error is showing right in the title line of the topology file. Is there any format issues ? I have attached the topology file mentioned in the error. Mohammad reza Afyouni Haldane model in condensed matter physics Hello everybody, I am new in topology in condensed matter physics. So excuse me if my question were somehow unusual. In Haldane model, we put one step (or steps) forward and take into account the annihilation and creation of the electron in the next-nearest neighbors in writing the Hamiltonian rather than the simple tight binding model, so my question is Why we do not take into account the annihilation and creation of the electron in the third, fourth and ... neighbors? Is this because those sublattices are far away ,so these hoppings are negligible? Thanks Clarence Lewis Protin Why do we need smooth structures rather than analytic ones in physics ? Consider the powerful central role of differential equations in physics and applied mathematics. In the theory of ordinary differential equations and in dynamical systems we generally consider smooth or C^k class solutions. In partial differential equations we consider far more general solutions, involving distributions and Sobolev spaces. I was wondering, what are the best examples or arguments that show that restriction to the analytic case is insufficient ? What if we only consider ODEs with analytic coeficients and only consider analytic solutions. And likewise for PDEs. Here by "analytic" I mean real maps which can be extended to holomorphic ones. How would this affect the practical use of differential equations in physics and science in general ? Is there an example of a differential equation arising in physics (excluding quantum theory !) which only has C^k or smooth solutions and no analytic ones ? It seems we could not even have an analytic version of the theory of distributions as there could be no test functions .There are no non-zero analytic functions with compact support. Is Newtonian physics analytic ? Is Newton's law of gravitation only the first term in a Laurent expansion ? Can we add terms to obtain a better fit to experimental data without going relativistic ? Maybe we can consider that the smooth category is used as a convenient approximation to the analytic category. The smooth category allows perfect locality. For instance, we can consider that a gravitational field dies off outside a finite radius. Cosmologists usually consider space-time to be a manifold (although with possible "singularities"). Why a manifold rather than the adequate smooth analogue of an analytic space ? Space = regular points, Matter and Energy = singular points ? Alejandro Gonzalez Gonzalez Which are the best books/articles to get acquainted with topological optimization and homogenization techniques? I know nothing about this two related subjects and I need, for the moment, a concise introduction and, later, a more deep explanation with implementation techniques. Rajwa Abdul Rezak Can anyone help me to create ligand topology files for GROMACS Protein-Ligand MD Simulation? Hello, I'm currently working on G6PD mutations and thus want to do molecular dynamic simulations for G6PD protein with its ligands: G6P and two NADP. However, I'm unable to create ligand topology files for the NADP ligand. I have tried ATB server, Lipargen server and swiss param. It would be helpful if anyone could help me with this. The LigParGen server is giving me the error as follow: "Sorry, an error has been detected in your input data (file, smile or selected charge): Found residue ligand NAP Unknown error. Please, check the input file. If you are not able to find the error, we suggests to use the SMILE code." The file I used is from molecular docking of ligands to the G6PD protein I modelled, I extracted ligands from PDB (2BH9). I added Hydrogens to the PDB file using Avogadro. Kalindu Fernando Why doesn't Topolbuild generate dihedral angle parameters at recommended setting for OPLSAA? Dear all, I am simulating a peptide with a few unnatural amino acids in Gromacs. I used Topolbuild to get topology files for the peptide. I cannot get dihedral angle parameters when I use recommended setting. May I know, why should I not get such parameters using recommended setting?
Liu Minyan How to smooth the results of topology optimization? Hi everyone, I am doing topology optimization in 3D, and I want to simulate and print the optimization result, but my optimization result has many steps, it is not smooth, so the exported STL file has a lot of meshes, I would like to ask if there is any way to make the topology optimization result smooth? Zuffain Hussan How do I set up Abaqus for topology optimization? We usually use Strain Energy as an objective with volume constraint in topology tasks. But if I want to reduce the mass/volume reduction of structure as much as possible until displacement along the 3 -direction is equal to -1. Did anyone know, how to do that? When I choose the (Displacement, 3-direction) minimum value in the design response, I get this error "The minimum operation cannot used be with the given identifier" How to deal with this? Thank you a lot! Vikas Kumar Fatal error: Syntax error - File LIG.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes ? Hello everyone, I am trying to simulate the protein-ligand complex with Zn ion but during solvation i am getting the following error: Fatal error: Syntax error - File LIG.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes I tried many ways but not able to solve this issue My topology file Topology file: ; Include forcefield parameters #include "amber03.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" ; Include ligand topology #include "LIG.itp" ; Include water topology #include "amber03.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "amber03.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_chain_A 1 Ion_chain_A2 1 LIG 1 SOL 27420 I also placed ligand itp file below forcefield parameters but it doesn't work. If you guys have any idea how to tackle this problem please help me. Thank you. Franco Magurno Gap partition in RAXML analysis at Cipres Gateway, how to deal with a mix of short and long sequences? I started to add recently the gap partition in my ML analysis of ribosomal genes because it improves the results. To perform my analysis I use the online version of RAXML at Cipres Gateway. I add the gap partition as binary data [1/0] with ascertainment_correction_lewis. However in my last analysis, where few short sequences were present together with other longer, I obtained an unexpected result. The short sequences clustered together, even if not related, in the wrong position and they were showing very long branches. An other short sequence was in the correct position but also showed a very long branch. The latter sequence covered the ssu-its part, where most of the gaps where present, while the formers covered part of the lsu. I deduced that the abnormal topology of the tree depended on the missing data in the gap partition, codified by '0' like the absence of gap. In other words the short sequences [not covering the its] had a big part of gap partition identical because of a long list of '0'. There is a way to overcome this problem without trigging the sequences at the same lenght? Mohamed Emad Barhouma How to simulate a graphene sheet using GROMACS ? Dear all,
I have tried to simulate graphene sheet as written in the website (https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up).
The reason I am trying to simulate the sheet, I want to add the graphene sheet as a substrate in a cubic box and evaporate some molecules on it.
Unfortunately, I had a problem while trying to run energy minimization using (gmx grompp -f minim.mdp -c GRM_w.gro -p grm_w.top -o min1.tpr)
I got the below error:
Fatal error:
number of coordinates in coordinate file (GRM_w.gro, 146535)
does not match topology (grm_w.top, 156815).
some differences between my simulation and the one in the website: 1. I am using gromos54a7 instead of charmm36.
The reason for using gromos 54a7 that I will need to evaporate some molecules on the graphene sheet and they should be evaporated using gromos 54a7. 2. I am using GRM instead of GRA.The reason for using the GRM is that I found the graphene sheet.itp online for the gromos 54a7 and it was named GRM and hence, I had to name everything GRM to match the names in the .itp that I included.
The steps I did using the terminal on Linux : 1. cd and go to directory 2. create a text file named GRM.gro and paste the data belwo in the file: GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring 4 1GRM C1 1 0.061 0.071 0.000 1GRM C2 2 0.184 0.142 0.000 1GRM C3 3 0.184 0.284 0.000 1GRM C4 4 0.061 0.355 0.000 0.245951 0.426000 0.284000 3. gmx genconf -f GRM.gro -o GRM_sheet.gro -nbox 15 10 1 create the graphene sheet 4. I created the file graphene.n2t and attached the below C CG2R61 0.00 12.011 1 C 0.142
C CG2R61 0.00 12.011 2 C 0.142 C 0.142
C CG2R61 0.00 12.011 3 C 0.142 C 0.142 C 0.142 5. I created a new file named grm_w.top and included the forcefield, the water model spc and the graphene sheet.itp that I found it online. ; Include forcefield parameters #include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/gromos54a7.ff/forcefield.itp" ; Include topology for GRA #include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/GRM4x.itp" ; Include water topology #include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/gromos54a7.ff/spc.itp" [ system ] ; Name GRM in water [ molecules ] ; Compound #mols GRM 1 SOL 50 6. I chanegd the size of the sheet in the z direction using: gmx editconf -f GRM_sheet.gro -o GRM_sheet_new.gro -box 10 15 10 7. I solvate the system using: gmx solvate -cp GRM_sheet_new.gro -o GRM_w.gro -p grm_w.top now the topology file grm_w.top was updated and a line was added as below: ; Include forcefield parameters #include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/gromos54a7.ff/forcefield.itp" ; Include topology for GRA #include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/GRM4x.itp" ; Include water topology #include "/home/abdelaal/Desktop/GROMACS/C60-TAPC/GRAPHENE/gromos54a7.ff/spc.itp" [ system ] ; Name GRM in water [ molecules ] ; Compound #mols GRM 1 SOL 50 SOL 48595 now I have 2 SOL which I don’t know what should I do. 8. I included in my minim.mdp file a line with : Periodic_molecules = yes 9. I tried to run energy minimization using: gmx grompp -f minim.mdp -c GRM_w.gro -p grm_w.top -o min1.tpr and I got an error: Fatal error: number of coordinates in coordinate file (GRM_w.gro, 146535) does not match topology (grm_w.top, 156815) END of steps.
I read that if the difference between the 2 numbers is devisable by 3, it means that the problem in the solvate and you can change the number manually to match the other one. But it is not the case here. I also thought that the problem might be that I have 2 SOL lines in the .top and I removed the SOL 50 line but the difference decreased by 149 only.
Looking forward for your help, I have been trying for many days without success. Attached are all the files I used it including steps file which contains all the steps I did as written above.
Abdelkrim Yassine Taki Eddine Dib Existence of a new function and its devlopement ? This paper is a project to build a new function. I will propose a form of this function and I let people help me to develop the idea of this project, and in the same time we will try to applied this function in other sciences as quantum mechanics, probability, electronics … Rodrigo Hidalgo-Linares In which cases we can interchange the inverse limits and the left adjoint functors? In the article "On the topology of a free locally convex space" by V. V. Uspenskii the exchange between an inverse limit and (which in my opinion is) a left adjoint functor is used. Specifically, if X is the inverse limit of an inverse system {X_\alpha : \alpha in A}, and F is a left adjoint functor, in which cases we have that F(\lim X_\alpha)=\lim F(X_\alpha). I know that the exchange occurs when we are taking direct limits (topological sums for example).
Salar J. Rashid Does the Mininet-WiFi emulator support multiple APs communication without a controller? We are working on the linear topology of multiple APs, but the connection between stations in different APs cannot be verified unless we add an SDN controller to the network! Is there any method to make this connection possible? because we want to compare the network in two cases: with and without a controller. Shams Eddin Mahmoud Alshorman Abstract algebra and topological algebra. If I wanted to link algebra and topology in order to specialize in algebraic topology (mathematics), what researches would you recommend me to start reading with? Thien Tran Calculate the sorbed amount of a molecule based on specific surface area? Hi all, I want to predict the sorbed amount of 0.5 M sodium sulfate solution with my ferrihydrite powder. The measured specific surface area is 190 m2/g. I also found the topological polar surface area of sulfate ions to be 88.6 A^2. I am trying to using the following number to calculate for the sorbed volume (Vm): S = [Vm*Na]/[mx22400], where N = Avogadro constant; m = mass of sorbent; a = cross sectional area of sorbate. However, I got a ridiculous result, so I am not sure which step did i do wrong? Or I should use another equation to solve this problem. Any input/suggestions are highly appreciated! Abdelkrim Yassine Taki Eddine Dib Riemann zeta function Problem and some questions ? Here we discuss about one of the famous unsolved problems in mathematics, the Riemann hypothesis. We construct a vision from a student about this hypothesis, we ask a questions maybe it will give a help for researchers and scientist. Giulia Trauzzi Running IMa3 on a SNP data set? Hello, I am trying to run the IMa3 software on my data set. I have a SNP data set. I have a feeling that the input format requires sequence data to infer the topology. Is there anyone who can help me understand what the input data would look like? Thanks Giulia Carlos Hernan Lopez Zapata The Kervaire-Milnor Formula and connection with the numerator of B2k/2k and the Turán moments for Riemann Xi function, ( Bernoulli numbers)? I am getting immersed in The Kervaire-Milnor Formula, where each term of which connects with a different field in mathematics: "The number of differential structures on the 4k − 1-dimensional sphere is given by a quantity that is the product of three quantities: Elementary factor × “Non − J Classes” × Numerator of B2k/2k". Information read in https://people.math.harvard.edu/~mazur/papers/slides.Bartlett.pdf My research is focused on how to connect the Turán moments and coefficients of Jensen polynomials for the entire function Xi as I have noticed some valuable results. I would like to count with more articles or information about the Bernoulli numbers visible in topics of topology which could involve the Turán moments and Jensen coefficients as well. Thanks in advance! Carlos Susheel Pangeni How do we fix badly or non equilibrated configurations in gromacs? Program: gmx mdrun, version 2019.1 Source file: srx/gromacs/mdlib/sim_util.cpp (line 752) MPI rank: 3 (out of 4) Fatal error: Step 700: The total potential energy is nan, which is not finite. The LJ and electrostatic contributions to the energy are 0 and 0, respectively. A non-finite potential energy can be caused by overlapping interactions in bonded interactions or very large or Nan coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology. Deepak Deepak How to generate topology file for ligand for Gromacs? Dear all, I converted a PDB file into Mol2 file using Openbabel (H added) and then fixed the bond order number using this command: perl sort_mol2_bonds.pl jz4.mol2 jz4_fix.mol2 When I try to generate the topology file for my ligand molecule using CGenFF server I get the following error message: "readmol2 warning: atom or bond number too high; skipped molecule..." (Screenshot attached) I get a different error on SWISSSPARAM for same file as following: "Failure report: It was necessary to change the name of the atoms numbered" (Screenshot attached) Could you please shed some light on what exactly could be wrong here to fix the problem? With this topology file, I wanted to run an MD simulation of the Protein+ligand complex. Many thanks, Deepak
Anup Vernekar Simulating Manhattan mobility with a large number (>50) vehicles in NetSim I want to simulate a grid-road topology (organized streets) with vehicles generate traffic to Road Side Unit (RSUs). Also, if I need to ramp up quickly to 100 or 200 vehicles how can I do that? Firyuza Bikinieva How to properly generate ligand topology for Gromacs? I have a problem with ligand-protein simulation in Gromacs. For research I need an MD simulation of the low molecular weight ligand and colchicine site of the tubulin dimer. Following Justin A. Lemkul's tutorial, I created a separate ligand topology file (using CGenFF) and a protein topology file. Probably because of the simulation of two protein alpha and beta chains, my protein topology file (topol .top) is different from the example topology file in Justin A. Lemkul's tutorial. Regardless of where in the topol. top where I write the parameters of the ligand topology, after creating the box and its solvation, the ligand is not rendered using PyMol. Also, the ligand topology data are absent in the solv.gro file after the complex solvation procedure. What am I doing wrong? Help me please Maxim Zaigraev How to automatically create topology of GPI-anchored Protein for Molecular Dynamics in Martini? Hello! For our research we need to do simulations of GPI-anchored proteins in membrane with Martini force field. But we don't understand how to generate topology for protein with covalent modifications in Martini. Can you help? We are working with three-finger neuromodulators (Lynx1, Lynx2, Lypd6, Lypd6b). Thanks in advance! Liu Minyan How to do topology optimization with moving asymptotes? I am currently doing a topology optimization of a given elastic tensor. My cost function is the square of the difference between the target elastic tensor and the elastic tensor, and my volume constraint is in the form of an equation, but I don’t know how to modify the MMA The parameters in make it applicable to least square optimization. I have read the notes of Professor Krister Svanberg and tried some, but still no success. Has anyone done similar optimizations? Can you give me a little help? Thank you everyone. Sanjit Dutta If we want to switch between two converter configurations each of different functions with common elements, what will be the best way? A combined topology of two converters with common elements is to be designed, where switching between the two converters can be done only when required (no importance of frequency of switching here). After switching ON/OFF each of the converters will be controlled differently and they will be completely independent. So if contactors are used, conduction losses would be higher. Even if semiconductor switches are used then we need a bidirectional and bipolar arrangement of switches, the number of switches will increase and the conduction loss in them will also be present. So I want to know what can be the other methods for this one-time switching because I want the path to be like the simple conductor with minimum or no additional losses. Or what kind of switching would be best here? Yunguang Wang Hi researchers, did anyone research the correlation between batcerial physiology status and its DNA topology structure before? Just as what I have asked, did anyone have done some research about this? I am so interest in it but I have no resource to do this, hoping someone had done and willing to share the result. Aniket Naha In Protein-Ligand Molecular Dynamics Simulation, how to resolve breakage of ligands after the 'grep' command ? Protein-Ligand Complex was generated after performing site-specific docking in AutoDock 4.2. I am following the MD-Tutorials by Justin Lemkul. Often bulky antibiotics are administered for therapeutic purposes. For building topologies for protein and ligands, both are separated using the 'grep' command. When the ligands are visualised in Avogadro, sometimes the ligands seem broken or distorted thereby unfit for topology building. I'm Using GROMACS 2020.1, CHARMM force field (Feb 2021), CGenFF server for building ligand topology. Kindly provide some suggestions to resolve the issue. Thanking you in advance Sushanta Sethi How can I create topology file from lammps data file? I need to create coarse grain (CG) beads from all-atom, for which I need to generate the psf file. To create the psf file VMD requires the topology file. So how can I create the topology file or Is there any other way that I can use to construct CG beads out of my all-atom i/p. Van Khanh Triet Nguyen Automate fixing topology errors using ArcPy? Dear all, After running the topology validation for the landuse dataset of a single district (polygon), I found over 2000 topology errors "must not overlap" in the data. I am wondering if there is possibility to automate the error fixing procedure with ArcPy. Because at the end of the day, I have to process landuse data for 20 districts at minimum. Thus, it might take months by using error inspector and manualy fix one-by-one. Thank you very much for any help & suggestion. Kind regards, Triet Top Gao Topological construction of peptide amidation in gromacs ? How to use gromacs to build topology after peptide C-terminal amidation ？ Sourangshu Ghosh Ricci Flow and Thurston's geometrization conjecture Hamilton defined the Ricci flow in 1982 to prove the famous three-dimensional sphere theorem. How singularities of solutions of the Ricci flow could identify the topological data predicted by William Thurston's geometrization conjecture? How did Thurston's geometrization conjecture eventually lead to the proof of the Poincaré conjecture? Cynthia Soto Whats is the difference between the SFT.R.sq vs truncated.R.sq values in the columns calculated by the soft threshold power function from wgcna? Dear connections I am testing several datasets using the wgcna tool. I am a bit confused with the meaning of two columns of the output table calculated for the soft threshold power function: "SFT.R.sq" vs "truncated.R.sq" columns. Please, let me please explain myself with two examples: Let's to suppose that I choose up the SFT power of 25 in the ntw1 (left plot - red-square) as show in the output table, the "SFT.R.sq" column sets this power with a value of 6.96911e-01, its convertion would be 0.1434, meaning that this value wouldn't adjust well to a free topology scale (TOM), but then the next column called "truncated.R.sq" has value of 0.6942. In fact an abline in 0.70 in the plot match the truncated.R.sq" as you can see. Thus, Why the too far distance between the two metrics? Now let's to see the next table on the right, focus on the SFT power of 28 (blue-square), the "SFT.R.sq" is ~0.74, but again the "truncated.R.sq" is ~0.913. Less distant but still with a moderate difference, Why? Please, somebody can explain to me, what is the more accurrate column's reference in this table to choose a SFT? and to provide a brief explanation of why? Thanks by advance Cynthia
Sunipa Sarkar Can I use Amber99sb-ildn force field for small molecule's topology? Hello Generally people use GAFF for the topology of small molecules. But I want to make the topology of small molecule using parameters from Amber99sb-ildn force field for a system where DNA will be simulated in presence of the small molecule. Is this a wrong way? Why people generally use GAFF for small molecule's topology? Please clarify my confusion. Thanks Elwin Heng Species Transport in Porous Media cannot pass through? I'm using ANSYS Fluent 2019 with Space claim, my problem is involving moisture diffusion (therefore using Species transport). I found that my h2o can never pass through the porous zone. I have tried varous porosity value, viscous resistance, with and without UDF of different diffusivity, and even (in space claim): shared topology or without shared topology but with contact. Do anyone know how to fix this? Braulio Villa Why the inyected current and grid voltage of my PV feded inverter can't be in phase? Hello, im workinmg on a single phase , single stage flyback solar inverter, i´ve been tryng with simulink and psim, in both simultations the output current can't be in phase with the grid voltage, in fact there is no active power in the output. Also when i measure the current in the input capacitor, there is a high current in it,. the input voltage and current reach the maximum power values, but it is like the capacitor is absorbing all the active powe, maybe that's relationated with the problem i used a PLL control, i've been trying with a lot of changes. The control used in the references is very simple and it works, i dont know what's wrong with my simulation.
Pradipkumar Goswami Which DC Transmission topology will be better if i want to transmit DC Power to a distance over 20 Km? My case is like i have 2 connection point which have operates on Grid of 400Kv 3 Phase voltage and i want to transmit power from 1 point to 2 point, the distance between 2 points is 20Km also the grid of both points are unsynchronised like have different frequency. I need the schematic Diagram for this transmission. I think first i need to convert from AC to DC at point 1 then need to Transmit DC from point 1 to 2 and then convert it back to AC from DC. So which DC Transmission topology i should use. and need schematic diagram for this. Rbah Yahya How to simulate Lora network applications in NS3? I need to simulate LoRa network applications in ns3 , in fact, i'm also looking for some examples of moduls that can provide the topology of lorawan network in ns3. Thank you, Sabin Poudel Which optimization is best while using PhyML phylogenic tree Topology/length/rate, Topology/length, length/rate, length, rate or none? I am trying to build the phylogenic tree using PhyML in Genious Prime and its offers me the Substutin model for which I used TN93, branch support bootstrap and for the optimize it has several options Topology/length/rate, Topology/length, length/rate, length, rate or none and I don't what they are and how it will affect my results. Can anyone help me to understand this. Kamal Aghayev IGBT or MOSFET is more suitable for use in 5-level cascaded h-bridge inverter? I'm simulating different modulation techniques based on the mentioned topology. Pallavi Agrawal Error in forming topology file in dna lignad complex in Gromacs? I am doing DNA ligand complex studies using Gromacs. I have use Amber sb ildn forcefield and make topology file for ligand using Acpype. It shows error that the solv.gro file and topol.top file have different atoms. i have used the following commands grep 'ATOM ' complex.pdb>| DNA.pdb grep 'HETATM ' complex.pdb>| ligand.pdb gmx pdb2gmx -f DNA.pdb -o DNA.gro -water spc -ignh -v -p topol.top Add H to ligand through pymol conda activate AmberTools21 antechamber -i Ligand.pdb -o Ligand.mol2 -fi pdb -fo mol2 -c gas python acpype.py -i Ligand.mol2 Merge DNA.pdb + updated Ligand_NEW.pdb -> Complex.pdb grep -h ATOM DNA.pdb Ligand.acpype/Ligand_NEW.pdb >| Complex.pdb cp Ligand.acpype/Ligand_GMX.itp Ligand.itp 3. `#include "Ligand.itp"` has to be inserted right after `#include "amber99sb.ff/forcefield.itp"`line and before `DNA_*.itp` line in _topol.top_. cat topol.top | sed '/forcefield\.itp\"/a\ #include "Ligand.itp" ' >| topol.top echo "Ligand 1" >> topol.top # Setup the box and add water gmx editconf -bt triclinic -f Complex.pdb -o Complex.pdb -d 1.0 gmx solvate -cp Complex.pdb -cs spc216.gro -o Complex_b4ion.pdb -p topol.top Create ions.mdp file cat << EOF >| ions.mdp Maria Solis How could I add harmonic restraint to Magnesium in *.itp for Gromacs? I generated files for minimization in Gromacs through Charmm-gui. But, when I was searching the bonds between Mg and amino acid in the section [bond], there were not. On the other hand, I could find possible interactions in the section [pairtype]. I would like to know if I could change the function from 1 to 6 in the section [pairtype] for harmonic restraints, because this change would not be possible according to the manual. https://manual.gromacs.org/documentation/2019/reference-manual/topologies/molecule-definition.html I attached my topology file Maria Solis FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE NN1? I am working on an protein-ligand system. I made a psf file and pdb with topology and parameters files of this only directory toppar_c36_jul20, but when I ran min.conf file in Namd , it generated that fault. Could someone help me ? Thanks you in advance. I attached the configuration file and the output Abhinay Thakur How to sort out the Segmentation Fault (Core Dumped) Error while performing EM steps in Gromacs? I am performing the EM steps (Gromacs Version 2021.1) but whenever I do so, I am getting Segmentation Fault (Core Dumped) Error. I have also even tried to reduce the parameter emtol = 100.0 ; Stop minimization when the maximum force < 100.0 kJ/mol/nm emstep = 0.02 ; Minimization step size nsteps = 200 ; Maximum number of (minimization) steps to perform But still, I am getting the same error for the past few days. I will be very thankful if anybody can help in sorting this error. Below, I am attaching the screenshot of the error file (.jpg), em.log.1 file, and topology file of mine molecule. Thanking You.
Yangmei Li Can I replace the atom charges generated by CGenFF with RESP charges so as to get more accurate simulation results? Hi, I would like to generate topologies for a couple of small ligand molecules. I have used the Ligand Reader & Modeler of CHARMM-GUI to do that. But the penalty obtained is too much, for example, "param penalty= 25.000 ; charge penalty= 45.141" for a protonated dopamine. I assume this is caused by inaccurate atom charges? So is it correct to directly replace them with (restrained electrostatic potential charges) RESP or RESP2 charges? Would it make the simulation results more accurate? Also should I change other parameters in the topologies accordingly? Super thanks! ref: Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2) Samir Touzani Is there a theory in topology in mathematics or in Geometry for NON-CONVEX sets? Convexe objects in Geometry are the most studied from elementary like squares polygons and so on. In advanced topology, Convex sets are the most studied and there prioperties are well and clearly defined. But what about Non Convexe in Geometry and in topology ? Is there classification and defined properties ? El AMRANI Brahim Conception of single-phase electronic dimmers ? I am an engineering student looking for sources regarding the design of monophasee electronic dimmers,Existing topologies, design methodology, complete diagrams realisation, explanations and practical implementation and thank you in advance Md Zubair Alam Emon How can we come up with a new circuit topology/idea for a DC-DC buck/boost converter? What is the approach? Should I propose/draw a new circuit and then analyze the voltage conversion ratio to find the performance. What are the steps? Any sort of help would mean a lot to me. Thanks. Yk Liu Whats does the following error mean in COMSOL: Warning: Forward solution failed, requesting reduced step ? Hello everybody I‘m using the topology optimization module to optimize a time-dependent phase change problem. After the first optimization step, these errors appear many times: Warning: Forward solution failed, requesting reduced step. Warning: Adjoint solution failed: requesting reduced step. can anybody help me, how can I solve this problem? thank a lot！ Maksymilian Szatko Problem with corect topology generation using Acpype? Hi, For quite a long time I've been trying to simulate polyphosphate ester molecules using GROMACS software with topology generated with Acpype, but with little success. The first approach resulted in an error from Acpype: ERROR: more than one residue detected '{'MOL', 'UNL'}' ERROR: verify your input file 'mol_att.mol2'. Aborting ... The input file for this attempt is attached to the post and named "mol_att.mol2". It is puzzling, since there is no MOL named residue. After some investigation the @ I tried to delete invalid fragment and run Acpype again, input file: “mol_noatt.mol2”. It gave me generated topology, but after minimization using parameters from em.gro the output was a distorted molecule. Is the problem with absence of the attributes section or there is another issue in my molecule that I did not spot? Best regards.
Mehdi Parsinia Properties of maximal subrings of rings of continuous functions In the recent paper which has been exhibited in the 51th Annual Iranian Mathematics Conference entitled "Notes on maximal subrings of rings of continuous functions" we give some properties of maximal subrings of some classes of subrings of C(X). However, we could not answer the following two important questions in this context. 1. Is every maximal subring of C(X) unit-free (i.e., whenever R is a maximal subring of C(X) and f is an element of R with empty zero-set, then f is a unit of R)? 2. Is every maximal subring of C(X) uniformly closed (i.e., closed under uniform topology on C(X))? I would be very delighted if you could let me your opinion about any ideas towards approaching the answers of these questions. Ed Gerck Regarding GR and QM? (SOLVED) In calculating the orbit of Mercury according to QM, it becomes open [1]. This is our answer to this question. A second answer is that GR requires QM. According to the Niels Bohr view, it is not that the universe is quantum ontologically, in its essence as Natur, but we give it an observed quantum model, and interpret it that way. "Physics concerns what we can say about Nature," explained Niels Bohr [2]. As one of the pioneers of quantum mechanics, Bohr explained further, that "there is no quantum world. There is only an abstract quantum physical description". In that sense, TR (topology reduction) by the author can be understood as providing the topological basis -- TR means "that a continuous path in a higher dimension must be discontinuous when projected in a lower dimension". TR does not change Wirklichkeit (nature as we oserve it), nor Natur (nature as unkown, unseen) as divided by Kant, in German. TR just changes how we observe nature. In that sense, TR changes physics -- Niels Bohr explained -- as physics concerns what we can say about nature, and there our description changes, although the facts remain the same. A similar situation happens with the number Pi, currently. We realize Pi as (3.141592...) is not measurable. Does it exist in nature, nonetheless? To give a short answer, NO. The universe is a non-euclidean space, where the ratio of a circumference to its diameter must stand as the ratio of two finite integers. The value is similar, may change according to the local curvature, but the curvature is never zero and we can use use finite digits for the ratio. Rather than a particular value, the quantum becomes a rule. This … changes GR, to a quantum basis -- what we were long waiting for -- harmonizing GR and QM. While not changing values very much locally, the long distance predictions can become very different. For example, the orbit of Mercury becomes open, as we published [1]. The precession of Mercury is a sweep, and Mercury can escape! And, with an open, spiraling out, orbit, Mercury can excite a sympathetic resonance with the Sun, wobbling in a growing faction, and even escape the Solar system in that growing orbit (see cosmological models). This could result in an exchange of orbital places of Venus <-> Earth, and the extinction of life on Earth -- by the growing temperature on Earth. This is unlikely, but now more possible. The consequences of investigating Pi -- even though Pi should not exist in nature, as an infinite precision number, thinking about it can be instructive Regarding GR and QM, what is your qualified opinion? Have we hit all the right reasons to modify GR, as in [1]? While not changing values very much locally, the long distance predictions can become very different. REFERENCES [1] https://www.researchgate.net/publication/339988557_On_the_Sun's_Gravity_and_the_Topology_of_Mercury's_Orbit [2] Petersen, A. The Philosophy of Niels Bohr. Bulletin of the Atomic Scientists, Vol. 19, No.7, 1963. Daria Solieva Can't generate a mash for topology in ANSYS. how to do it? Created model of steel caisson in space claim. Used a static structure for topology. But there's an error "one or more surfaces cannot be mashed with acceptable quality", " One or more entities failed to mash". How to solve, please help Cassie Sims Charmm/GROMACS Residue 'ZN' not found in residue topology database? I am trying to do some MD simulations of a protein with zinc ions. I am trying to use a charmm forcefield (I have tried 2017 and 2021) and Gromacs. I get an error when doing pdb2gmx Residue 'ZN' not found in residue topology database ZN is in the force field files for Charmm so I am not sure what to do! Thanks in advance. John Nguyen How to perform alchemical free energy calculations in GROMACS? I am looking to calculate the difference between the binding affinities of two isomers of a molecule bound to a membrane embedded protein using a method similar to this in GROMACS: http://www.mdtutorials.com/gmx/free_energy/index.html In the tutorial, the transformation is entirely controlled by options in the .mdp file so it's not necessary to specify a B-state in the topology. However in my case where I'm transforming a trans double bond to a cis, I think I would need to include both states in the topology but I'm just not sure how to exactly do it and what .mdp options are needed. Any help/references would be much appreciated. Xia Zhenyang Any example about fixed point theory being used to prove some questions in symplectic geometry ? As question stated , maybe can also include symplectic topology. Ankan Ghosh Dastider What is the best simulation platform for Topological Insulator-based devices? Topological insulators (TI) can be incorporated into various devices with superior characteristics as per the recent literature. How can these characteristics be explored via simulation? May I know some of the best platforms to start simulating various characteristics of TI-based devices? Shalaka Sitre %THD analysis of Multidrive system under balanced load condition in 0-2kHz So I made a multidrive system of upto 20 drives with balanced load conditions. I am monitoring the %THD in the drives with different topologies. I have to consider different load profiles (low power units, medium power and high power). What power ratings of the load should I use? Kouider Bendine CFD simulation of HVAC filters ? Dear All, I am working on a project to improve the filtering efficiency of HVAC filer type ePM2.5. My main idea is to decrease the pressure drop caused by the filter by working on the filter shape. Therefore, I am planning to optimize the filter shape using topology and shape optimization in a CFD simulation. I have never performed such never conduct a CFD simulation of filters before. so any kind of hint or clarification or tutorial regarding the filter CFD simulation and optimization will be extremely helpful. Thank you in advance Dikran Dikranjan Does the Addition theorem hold true for the topological entropy of continuous endomorphisms of locally compact abelian groups? The topological entropy h(f) of continuous endomorphisms f of locally compact groups was defined by R. Bowen (in the metrisable case). One says that the Addition theorem holds for a continuous endomorphisms f of locally compact group G if for every f-invariant closed normal subgroup of G the topological entropy h(f) of f coincides with the sum of entropies h(f|_H) + h(f'), where f' is the induced endomorphism of G/H. Bowen established the Addition theorem for compact metrisable groups G, this was proved also by S. Yuzvinski somewhat earlier. In 1981 a proof containing various gaps of the Addition theorem for LCA groups was proposed by J. Peters. So far no correct proofs are known to the best of our knowledge. Prateek Kumar How to obtain parameters for ffnonbonded.itp file while adding a residue (Such as NAG) to forcefield? I have generated the topology file for the residue and modified the residuetype, atomtypes files but not able to modify ffnonbonded file. Could you please help me out in this. Thanks in advance. Pallavi Agrawal Error in forming topology file in dna lignad complex in Gromacs? I have added 1.AMBER14SB_parmbsc1 2: AMBER99 force field BSC1 in my working directory but it still gives the error- Residue 1 named DG of a molecule in the input file was mapped to an entry in the topology database, but the atom C5' used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. I have given command to change clean.pdb file to processed.gro file but it still gives the error . Clarence Lewis Protin Can we characterise essentially interconnected digraphs ? I call a digraph G= (V,E) essentially interconnected if whenever any vertex $a$ is removed from $G$ there is always at least one pair of distinct vertices $v$ and $w$ which can no longer be joined by an oriented path in $G$. Are there essentially interconnected graphs ? Example: The cycle: (a,b), (b,c),(c,a) If I remove $b$ then I cannot connect $a$ to $c$ (although I can connected $c$ to $a$) and analogusly for $a$ and $c$. Can we characterise such digraphs in general ? Edward Jenks How do you mesh a thin solid in Fluent? Hello, I have used the shell function on SpaceClaim to create thin solids for the model I am studying. These are contained within an enclosure for my study. I chose this approach as it avoids the need to define any inlet or outlet boundary conditions that are unknown. Unfortunately, I have been completely unable to mesh the thin solids within the enclosure. An error message isn't thrown, as the mesh never finishes. So far I have tried a range of meshing methods and also shared topology but I haven't had any luck. Is there a specific way that I can tackle this problem. (When I just run a surface mesh on the thin solids alone, it works fine, so I don't think it's a geometry problem). Many Thanks Emmanuel Anuoluwa Bamidele Can I consider the OOB score of RF model as the same as R^2 score? In a topology optimization machine learning prediction algorithm, can I consider the OOB score of RF as the same as R^2 score. Could that be a more unbiased way of validating the model Iman Katouzian Cellulose topology file? Good day. I got a .cif file from a supplementaryfile in a paper, related to cellulose molecule which I want to use in my simulations. I run this code to change the format to pdb file for input of pdb2gmx code -----> babel -icif ncellulose.cif -opdb ncelluose.pdb However after getting the pdbfile and runningpdb2gmx -f ncellulose.pdb I get error :
Error in user input:
Invalid command-line options
In command-line option -f
File 'ncellulose.pdb' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
I also checkedthe onlineAutomated Topology Builder (ATB) and Repository and again the topology file cannot be built and it says that the file is invalid.
Can somebody help on this issue I want to use this cellulose file for my simulations.
Please find attached the .cif and convertedpdb files.
Thanks. Bhukya Bhavsingh Inductive Wireless power transfer in ev battery charging? Dear sirs/madams, I am selected for compensation topologies in my research, in wireless power transfer in ev battery charging. Please suggest how to proceed and how to achieve soft switching by using compensation topologies Please respond sirs/madams Thank you Douglas Diehl Lipid Force Field with gromacs command pdb2gmx? I have a pdb file that contains DPPC molecules and other molecules. I want to generate .gro and .top files from this pdb file using the Gromacs command pdb2gmx. I am trying to use the Charmm36 force field (update jul20), which contains atomistic topologies for DPPC. The problem is the DPPC atom names in my pdb file are not being recognized - i.e. Fatal error: Atom N4 in residue DPPC 1 was not found in rtp entry DPPC with 130 atoms while sorting atoms. Is there a way around this? Maybe I need to put the pdb file together in another way or use a different force field. Any suggestions would be appreciated. Debjit Mullick How much is needed to paint a Möbius wall ...??? Discussion If someone (a painter) claims that he /she will charge ₹5000 to paint the inner part of a wall , surrounding a cricket ground &that for the outer part of it is ₹7000 ... What if the maker of the wall makes it in a shape the of a möbius strip ....???? Philip Tobianto Daely Is it possible to dynamically adjust the data rate of a wireless node using TSCH protocol in Link Layer? I'm currently learning about rate-based congestion control for industrial wireless sensor network. Suppose there is a network consisting of several sensor nodes and one coordinator node connected in star topology (coordinator as a center of topology). Periodically, sensor nodes will transmit sensing data to the coordinator node. The algorithm that I'm working on is designed to change the transmission rate of each sensor nodes every time a congestion occur (coordinator receive too many packets within a short time, hence making the receiving buffer overflows). As this algorithm is intended for industrial wireless sensor network, I want to try to combine them with WirelessHart and ISA100.11a protocol. As both protocols are designed over IEEE802.15.4 protocol with Time-Slotted Channel Hopping (TSCH) in its Link Layer, the transmit rate will be dependent on the timeslot size in slotframe. Hence my current conclusion is that: during network operation, if my algorithm wants to change a node's transmit rate, my algorithm must be able to change the TSCH timeslot size. Is it possible to implement my algorithm to TSCH devices currently on market? Is it recommended? Or does my conclusion not correct? Alexander Müller Floating current source, literature? Hello guys im looking for a way to implement floating current sources in my circuit referring to the following topology https://www.semanticscholar.org/paper/A-fully-differential-class-AB-OTA-with-CMRR-by-Centurelli-Monsurr%C3%B2/fefedc5e9204b0b80f8d1d6349db65b44964a868/figure/0 . I checked all the papers concerning this topology and this floating current sources are not mentioned at all. If someone knows some good literature i would be gratefull. Kind regards Sergei Turanov What inherent features could explain the differences in topologies produced by NJ and BI methods? Dear colleagues! Recently when reconstructing phylogenetic trees based on COI gene for species identification purposes I noticed the strict inconsistency of the topologies produced by neighbor-joining (NJ) and bayesian inference (BI) methods. As you can see on a figure NJ produce clear species bifurcation whereis BI forms stem cluster. It is only typical for the species with low interspecific divergance (below 2%). What are the inherent features of these algorithms to make such inconsistency? Any ideas on BI behaviour? I do not ask what is true or which algorithm is best. I'm curious what features of BI (for instance) could explain this. Thank you! P. Karthiksankar What is the current research area in Topology? I wanna do research in Topology, So I wanna know correct research area in Topology. Yaroslav Ivanovich Grushka On continuity of inverse operator and uniform convergence :)? Dear colleagues. The text of the question is available in the attached image or pdf-file. Sincerely, Yaroslav Grushka.
Zahra Chavoshpour How converted *.inp charmm file to *.top Gromacs file ? I want to simulation cytochrome C that it has two parts HEME and protein. I have charmm files par_heme.pdf and top_heme.pdf heme group but I do not know how to convert pdf file to *. inp because the paper said these are charmm file *.inp. also, I want to combine top par files for protein and heme to one and convert to Gromacs topology file. I searched and found I could with psfgen and top tools plugin in VMD. I do not know how to use vmd about it. Robert Shour Should graphical representations of networks converge for thermodynamic reasons? Some excerpts from the article Comparing methods for comparing networks Scientific Reports volume 9, Article number: 17557 (2019) By Mattia Tantardini, Francesca Ieva, Lucia Tajoli & Carlo Piccard are: To effectively compare networks, we need to move to inexact graph matching, i.e., define a real-valued distance which, as a minimal requirement, has the property of converging to zero as the networks approach isomorphism. we expect that whatever distance we use, it should tend to zero when the perturbations tend to zero the diameter distance, which remains zero on a broad range of perturbations for most network models, thus proving inadequate as a network distance Virtually all methods demonstrated a fairly good behaviour under perturbation tests (the diameter distance being the only exception), in the sense that all distances tend to zero as the similarity of the networks increases. If achieving thermodynamic efficiency is the benchmark criterion for all kinds of networks, then their topologies should converge to the same model. If they all converge to the same model when optimally efficient, does that cast doubt on topology as a way to evaluate and differentiate networks? Diptendu Roy Could I use topology file created by vmd for doing md in gromacs? I am facing a problem to make topology file using cgenff as instructed in Lemkul's Gromacs tutorial. But it didn't work as I couldn't get Networkx of version 1.11 . So, I am trying to find an alternative way. I made my topology file using autopsf builder of vmd. Could I use this topology file for MD simulation in gromacs? I am very new in this field. Please help me. Thanks in advance for any help or suggestions. B.K. Tripathy What is the fundamental difference between KSOM and LVQ models? The Kohonen self organising maps(KSOM) and the Learning vector quantization(LVQ) both classify patterns. It is said that both these two being that the topological structure at the output unit is not being considered in the case of LVQ. I would like to have a better explanation of the difference, if possible example to illustrate. Sunnykumar Jagani Which software is good for topology optimization? I have to use different software such as - Solidthinking Inspire - Creo 6.0 -Simens NX - Optistruct. so which one is better for on point of result and surface finish. thanks Payal Wadhwa Why there exists four Z2 invariants for a three-dimensional topological insulator (TI) and one Z2 invariant for a two-dimensional TI? As Kane Mele suggested that there exists four Z2 invariants for a three dimensional topological insulator (TI) while only one for two dimensional TI. But what is the reason for the same? Monalisa Singh Roy What are some "smoking-gun" signatures of topological phases in low-dimensional number-conserving systems? In low-dimensional systems, e.g., one-dimensional (1D) Fermi wire with proximity-induced superconductor pairings, exponential ground state degeneracy is taken as a hallmark of underlying topological phase with localized edge modes. Entanglement spectrum showing degenerate eigenvalues, and exponential decay of Question: What would be some good criteria to 'recognize' topological phases in gapped number-conserving systems in low dimensions? Some context: We explored a 1D Fermi gas with attractive interactions ( Article Fermion parity gap and exponential ground state degeneracy o... Article Topological States in a One-Dimensional Fermi Gas with Attra... Jiaxing Zhu The application of the criterion to detect the runaway reaction in semibatch reactor in the industry There are many criterion proposed in the literature( such as the target temperature boundary, topology criterion). The latest development and limitation of criterion and its application in indudstry Muhammad Ikhsan What are the dominant converter topology people usually used for small wind turbine with PMSG? Hello Technician and Academician Can somebody please inform me, what is actually the type/topology of power converter available at the market for small wind turbines (below 10kW) with PMSG? especially for the rectifier part, is it just simple rectifier or controlled rectifier, with thyristor or MOSFET? what are the dominant topology people used? for offgrid and ongrid if you check IEEExplore, then soo many types, but I cannot find the reality in the market what people recently use actually? Best Regard Ashrith Bhat Thirthamutturu Ramaswamy In Abaqus- How to optimize the shape of a particular region while keeping displacement at two points equal? I am new to abaqus and I am trying to optimize a shape of a segment of a model (As a part of my master thesis). Please refer to the example model I have attached. I need to optimize the segment which is in red color keeping two black colored segments parallel. I have tried all the options in "Geometric constraint" in "optimization" tool but none of the options seems to give this parallel constraint. I do not want to reduce the volume ( hence Topology optimization is not required). Hence trying with "Shape optimization" option. Any help would be appreciated. Thank you in advance.
Payal Wadhwa How can we determine the weak topological phase in 3D topological insulator? Dear all, Can somebody please tell me that how can we determine the weak topological phase in a topological insulator in 3D? Firstly, i calculated first Z2-index v_0, which comes out to be zero. but it has even no. of dirac cones, indicating that it may be a weak topological insulator. So, how can i determine the other three indices? Whatever i read, i understood that we have to check Z2 for three different planes like (001) (011) and (111). Z2 for which plane comes out to be 1, that would be the corresponding weak topological phase. Suppose for (011) Z2 is 1, then (0;011) would be the weak topological phase. I don't know whether i am right or wrong. Kindly correct me, if i am doing something wrong. Thanks in advance! David Adjei What are the topological properties between a Sphere and a Hollow Sphere? I'm trying to figure out the topological properties of the above surfaces. Thank you Dimuthu Kodituwakku How to build a topology for a novel molecule in CHARMM? Hi, I'm trying to attach a carbonyl linker to Lys so that I can attach a PEG molecule to it. I have attempted so far by combining Lys , N-terminal and C-terminal topology data . But I'm having trouble deciding on the atom types I should use and the charges. Also whether I should stick to using CGENFF.
Linker and part of Lys topology file I have combined so far,
ATOM CE CT2 -0.20
ATOM HE1 HA2 0.09
ATOM HE2 HA2 0.09
ATOM NE NH1 -0.70
ATOM HE HC 0.44
ATOM C C 0.51
ATOM O O -0.51
I have also attached my molecule below. Any help would be appreciated, Thank you
Ravi Saini Calculation of mmpbsa (on gromacs files) Its been long people are using rashmi Kumari tutorial for calculating mmpbsa. But real problem comes when we generate file using latest gromacs (in my case its gromacs 2020.3) and try to calculate mmpbsa. rashmi Kumari tutorial supports end with gromacs 5.1.x and i have tried parmed.gromacs as well but everything fails. If someone can help me in learning how to calculat mmpbsa with files obtained from gromacs 2020. It will ne a great help. Tao Rongkun Are there any good type II membrane protein signal peptides for mammalian cells? I am currently working on membrane protein topology research with fluorescent protein. I found so many type I membrane protein signal peptide (SP), like PDGFR or GPI domain, but very few type ii SP. I wonder if anybody could recommend some good type II membrane protein signal peptides. Thank you so much. Kandula Eswara Sai Kumar Topology optimisation for dynamic loads in OptiStruct? Is there any material available for topology optimization of a structure using OptiStrct under dynamic loading conditions? Thanks in advance. Cedric Salame How do we use polarization in Gromacs 2019? It seems that polarization has been implemented in the Gromacs version of 2019 and further. However, I can't seem to find relevant info in the documentation except for the edits that have to be done to the topology files. Do we have to work to do edits to the other parameter files? |
