Science topics: Mathematical SciencesTopology

Science topic

# Topology - Science topic

Explore the latest questions and answers in Topology, and find Topology experts.

Questions related to Topology

I'm studying about strict binary tree topologies and I found a way to check how many possible topologies it is possible to build given

*n*number of leaves of the tree. The equation for this calculation is as follows:However, this above equation returns the number of possible topologies given

*n*, including mirrored trees. I need to know the amount of possible non-mirrored topologies.I found a very interesting article (below) that seems to show the calculation of number of possible topologies given

*n*for non-mirrored trees, but I didn't understand how to calculate it. Can anyone help, showing in practice for*n*= 10 and*n*= 11? Thank you very much and sorry for my bad english.Dear all,

I have been finding several published papers on soft set, soft topology and hybrid structures. In early days of my career in soft topology, I also worked with notions of Cagman et al., Shabir and Naz, etc. But, I must admit boldly that ideas of soft set theory, soft topology, etc. defined by others are incorrect. Prof. Molodtsov raised questions many times on available notions of soft empty set, soft absolute set, etc. He showed disagreements on these notions which carry no sense of soft set in reality. Prof. Molodtsov had disagreements on operations of soft sets, soft mappings, etc. His arguments and disagreements were published in several journals, but I am sad to say that soft set researchers community never tried to find Prof. Molodtsov, the father of soft set, along with his works on soft sets.

Thus, I am bold enough to ask following questions to researchers of soft topology:

1) How can you claim that you are following correct notions and meanings of soft topology?

2) Have you ever tried enough to search about Prof. Molodtsov and his published papers post 1999's soft set theory before publishing rubbish ideas in spite of the fact that Prof. Molodtsov showed us correct path in soft set, soft topology, soft rational analysis, etc.? The published papers of others are not contributing any correct idea to soft set theory and hybrid structures by anyway. These papers are simply misleading young researchers because of some arrogant researchers of soft set theory who are desperately ready to reject ideas and advices of Prof. Molodtsov, the father of soft set theory just for publication bof their ideas or to increase citations.

Thus, I request editors of journals to stop publishing incorrect ideas of soft set theory. I also request publishing houses to encourage correct notions and ideas of soft set theory and hybrid structures. I also request American Mathematical Society, European Mathematical Society, etc. to take initiative to organise conferences on soft set theory for the discussion of correct structures of soft set, soft topology, etc. I am available for debates on correct structures of soft set theory and related ideas in international conferences if one is ready to debate. I just want that soft set theory and hybrid structures must be developed using correct ideas of Prof. Molodtsov.

Thanks

Santanu Acharjee, PhD

(Collaborator of Prof. D. Molodtsov,

Title of the paper: Soft rational line integrals, published in 2021 and two more in submitted form)

Assistant Professor

Department of Mathematics

Gauhati University, India

I'm running 100 ns long MD simulations of a small peptide in isolation or bound to a partnering protein. My goal is to produce a plot of the residues in double helical form from start to end along with a video of the structure using Chimera.

The steps I take after a MD run are...

Step 1:

Center the trajectory file:

gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center

--- Type 1 for protein and then on the next prompt 0 for system.

Step 2:

Calculate the back bone rmsd of the entire complex:

gmx rms -s em.tpr -f md_0_1_noPBC.xtc -o rmsd_xtal.xvg -tu ns

--- Type 4 then 4 for backbone RMSD calculations

Step 3:

I then make an index file of the two chains:

gmx make_ndx -f md_0_1.gro -o index.ndx

--- Type "splitch 1" hit enter, type the number of what chain I want to reference (typically "2"), then type "q" to exit

Step 4:

From there I want to produce a trajectory file (.xtc) from the index and an updated topology (.tpr) file from my MD run using the index file:

Step 5:

Trajectory of just chain 2:

gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -n index.ndx -o chain2_traj.xtc

--- Type the chain I want to reference (typically "19")

Step 6:

Topology of just chain 2:

gmx convert-tpr -s md_0_1.tpr -n index.ndx -o md_chain2.tpr

--- Type the chain I want to reference (typically "19")

Step 7:

I then center the updated files:

gmx trjconv -s md_chain2.tpr -f chain2_traj.xtc -o chain2_traj_noPBC.xtc -pbc mol -center

--- Type "1" then "0"

Step 8:

I then perform my analysis using dssp and rms

gmx do_dssp -f chain2_traj_noPBC.xtc -s md_chain2.tpr -sc scount_chain2.xvg -o ss_chain2.xpm -dt 10 -sss H

--- Type "5" for mainchain

Step 9:

gmx rms -s md_chain2.tpr -f chain2_traj_noPBC.xtc -o rmsd_xtal_chain2.xvg -tu ns

--- Type "4" then "4" for backbone rmsd

*** The issue I run across is when I open the tpr and xtc files in Chimera with the MD viewer, the peptide is completely wrong. What I've deduced is that the topology (tpr) file for some reason gives each atom in the first few residues their own residue id's. Thus residue 1 actually makes up residues 1-9 (or something similar). However, when I produce a pdb from the trajectory file (.xtc) with:

'''

gmx trjconv -s md_chain2.tpr -f chain2_traj.xtc -dt 100 -o trj.pdb

'''

The peptide is correct. So I believe the issue is that the topology file is being produced improperly due to a bug or something wrong with my steps above. I've also tried using the em.tpr file for input on step 6, but I run across the same issue. This is happening with several different peptides. One peptide that is 65 amino acids long and one that is 18 amino acids long. On the 65mer, it appears to only happen on the first 4-5 residues. ***

I am starting a new area of research that is Algebraic topology. Kindly suggest some latest problems and related publications

I am trying to generate OPLSA topology for LiTFSA using LigPargen tool. But it is showing an error. Are there any other tools for generating OPLSA topology parameters in Gromacs?

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?

Suppose, If I am doping a topological insulator let's say Bi2Se3 with an external magnetic ion whose spins order in-plane (easy axis in ab plane ), what could be the corresponding changes in the Dirac cone below the ordering temperature?

As asphalt has various components, how do we create a topology for asphalt.?

I am doing research on topology optimization, filling a unit lattice with different materials, and I want to use the homogenization theory to calculate the static effective elasticity tensor of the unit cell, as shown in the file .

How to set comsol to calculate E33 in 2D model?

Usually, systems, where conduction electron acquires a berry phase due to noncoplanar spin structure, are topological hall effects. Is the geometric hall effect another name for the same effect?

"In crystalline solids, where the wave vector k becomes a good quantum number, the wave function can be viewed as a mapping from the k-space to a manifold in the Hilbert space (or in its projection), and hence the topology becomes relevant to electronic states in solids" - This is a statement in the introduction of Yoichi Ando's comprehensive review on topological insulators. Ref: Ando Y., Topological insulator materials, J. Phys. Soc. Japan, (2013),

**82**, 102001.I find it difficult to understand why k being a good quantum number allows for the wavefunction to be viewed as a mapping from k-space to a manifold in Hilbert space. I would appreciate to receive some insights on the statement given in quotes. Other approaches to explaining why Hilbert space topology becomes relevant to electronic states in TI are also welcome. Thanks in advance.

1. In a TI surface state/edge state, each k state exists in pairs. The Dirac cone in a 3D-TI has a -k state for every +k state.

2. Due to spin-momentum locking caused by high Spin Orbit Coupling (SOC), the -k state will possess opposite spin to that of +k.

Am I correct in understanding that the combination of these two conditions is what makes the system be termed as a time reversal symmetry protected system? That is, k needs a -k (Kramer degeneracy), and the -k state is opposite in spin also. Hence a TR operation completely reverses the state.

If yes, my question is the following:

What physical properties (band structure, crystal structure) of a system causes a material to possess the Kramer degeneracy? That is, physically what causes a material's band structure to possess k states in pairs?

But, the kramer degeneracy theorem is defined as: 'every eigen state in a TIME REVERSAL SYMMETRIC system with half integer spin will have at least one other degenerate eigen state'. This definition makes it seem like TRS is one of the requirements for the kramer degeneracy.

I am confused about which is the cause and which is the effect here? Does TRS cause the Kramer degeneracy? Or is the presence of the Kramer degeneracy along with spin-momentum locking causing the system to be called time reversal symmetry protected?

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**?Does anybody have any idea how to execute an user defined python script in the middle of a mininet wifi script just after the topology is created and then manipulate the nodes based on the results of user-defined python script. Please help. If anybody knows then please send me the steps or an example script.

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 Wikipedia ( 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.

- Khamehchi et al., “
**Negative-Mass Hydrodynamics in a Spin-Orbit–Coupled Bose-Einstein Condensate”,**2017 - https://www.researchgate.net/profile/Thomas-Busch/publication/311612111_Negative-Mass_Hydrodynamics_in_a_Spin-Orbit-Coupled_Bose-Einstein_Condensate/links/5a97b63845851535bcdee6fd/Negative-Mass-Hydrodynamics-in-a-Spin-Orbit-Coupled-Bose-Einstein-Condensate.pdf

I am screening few drugs against a targeted enzyme using autodock 4.2, i had obtained best conformation now in order to perform MMPBSA, i am working with Gromacs.

The pdb file for the selected cluster was obtained by saving the cluster in .pdbqt format later i had opened the file in pymol and re-saved the file to .pdb....now by following standards tutorial available from the Gromacs tutorial, after seperation of both the pdb, and converting the ligand pdb to .mol2 formate when i used swiss param web site for generating topology file for ligand it was showing error.

So question is should i use the same ligand.mol2 from the autodock generated cluster or can I proceed by re-downloading my ligand file from zinc data base and continue my stimulation or should I should use the ligand coordinates that i got from autodock Vina....."as i am facing trouble to generate the topology from coordinates that i was obtaining from the autodock 4.2 is there any solution to fix it"

Hello,

I am currently working on something that requires cycle accurate simulations (TLM) for NoC that contains Irregular Mesh Topology(ies) / completely arbitrary topology(ies).

Also routers should support X no. of ports instead of standard no. of ports.

Could you please name a few free simulators that support the above mentioned features.

Thank you in advance & best regards

Manikanta

I want to know about introduction, definition, explanation, examples and application of soft multi set topology

Hi ,

I am facing some problems in my ligand-protein (docked complex) simulation.

-------------------------------------------------------

Program: gmx grompp, version 2019.5

Source file: src\gromacs\gmxpreprocess\grompp.cpp (line 610)

Fatal error:

number of coordinates in coordinate file (complex_solv.gro, 61208)

does not match topology (topol.top, 61207)

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

-----------------------------------------------

I already searched on the internet and tried to figure it out by myself but couldn't. I am attaching the topology and gromacs files too.

Please help me figure this out if anyone can. Thanks

Hello everyone,

While performing MD simulations of protein - ligand complex, at the adding ions stage I am facing an error :

Fatal error:

Syntax error - File UNK_fix.itp, line 7

Last line read:

'[ atomtypes ] '

Invalid order for directive atomtypes

Well, since I've used Swissparam to write the topology file of the ligand (UNK_fix.gro) which usually uses CHARMM all atom forcefield and the protein topology I've written with the charmm36-2019.ff. Can this be a reason that I'm facing the above error?

I've also referred to other options like #include statements which I suppose are correct and the editing in topology is all done right. For reference:

; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

; Include ligand topology

#include "UNK_fix.itp"

; Include water topology

#include "./charmm36-mar2019.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 "./charmm36-mar2019.ff/ions.itp"

[ system ]

; Name

Protein in water

[ molecules ]

; Compound #mols

Protein 1

UNK 1

SOL 24553

So, please guide me through any other suggestions which may correct this error.

Thank you in advance!

While running the command gmx mdrun -deffnm nvt I was facing an error

Step 0: The total potential energy is 3.94046e+16, which is extremely high.

The LJ and electrostatic contributions to the energy are 3.94046e+16 and

-1.10841e+06, respectively. A very high potential energy can be caused by

overlapping interactions in bonded interactions or very large coordinate

values. Usually this is caused by a badly- or non-equilibrated initial

configuration, incorrect interactions or parameters in the topology.

how to overcome this please help me out

I aws running the command gmx grompp -f ions.mdp -c 1ua7_solv.gro -p topol.top -o ions.tpr -maxwarn 1 but I encountered an error stating number of coordinates in coordinate file (1ua7_solv.gro, 90855) does not match topology (topol.top, 90854). How to overcome this . Please help me out . I am attaching both the files and screenshot of the error.

During the topology generation of protein (PDB id: 6lu7), a fatal error occurred. How to resolve this error and what precautions should be taken to avoid such errors?

Thanks in advance.

Regards,

Vinay

Hi, everyone! I developed a ML tree using IQtree, then I uploaded output file (.treefile) into itol and Figtree. I got different tree topologies using itol and Figtree. Any idea why? If someone could assist me, I would be grateful. Thanks :)

Dear researchers

I try to perform molecular dynamics many times, but I get the following fatal error - UNABLE TO FIND ANGLE PARAMETERS FOR CG2R61 NG2RC0 NG2RC0 (ATOMS 4981 4986 4977). I attach the .pdb-file (for protein-ligand complex) and .str-file with topology of ligand (by CGenFF). Please help me to fix this error.

i was running the energy minimization step using the command gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr in gromacs but the error occurred of mismatching of atoms how to correct this? I am attaching both the files of topology and em.gro

thanks

Hi, I tried to do topology optimization on wheels as part of my dissertation trying to make light weight wheels for a student formula car but don't understand what I'm doing wrong. I'm using ansys

getting .str file for a given molecule through CGenFF is almost a simple task but how we can further achieve the topology and parameter file for actual tasks.

Even after including all the forcefields in the topology file still facing this issue. I am attaching the files supporting. Complex is intact with ligand but while adding ions :

gmx grompp -f ions.mdp -c solv_sp.gro -p topol.top -o ions.tpr

Facing the error

Fatal error: Syntax error - File ffnonbonded.itp, line 1 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes?

Please guide with your suggestions

Thank you in advance!

I have prepared a new Cd based MOF. I want to do some topological analysis. Is there any software available? Any help will be greatly appreciated.

Hi everyone,

I work on Abaqus for a project and I want to optmise a part (topoogy + shape). I created the model an ran the topology optimisation. Now I want to extract the result geometry to make some shape optimisation. Is it possible to make it directly from Abaqus or with a Pyhton script or do I need to convert it in a CAD software ?

Thank for your help

I have a streel structure and the welds need to be merged in share topology in SpaceClaim in order for the elements of both parts to match.

But the contact between beam must no be merged in shared topology so that I can make a contact frictionless in Mechanical.

I can only manage to either separate all bodies so that they all make contacts (but mesh does not match) or merge all bodies so that mesh matches (but no contact surfaces are created and I cannot make the beam-beam contact frictionless).

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.

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?

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)

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

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.

For writing research articles

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.

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

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 ?

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.

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.

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?

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!

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.

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?

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.

*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 …*

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).

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.

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?

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!

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.

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

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

Program: gmx mdrun, version 2019.1

Source file: src/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.

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*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

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!

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.

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?

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.

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

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.

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

How to use gromacs to build topology after peptide C-terminal amidation ？