[gmx-users] generic hardware assembling for gromacs simulation

Dear Benson, Thank you for answering . I am using Centos 6. My current simulation time for protein-ligand systems is about 1.6 ns/day. I am wondering if installing the GTX 1050 or GTX 970 can boost the output significantly (maybe 2 or 3 times more ?). I am installing just as mentioned below. tar

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 63

Dear Benson, Thank you for answering . I am using Centos 6. My current simulation time for protein-ligand systems is about 1.6 ns/day. I am wondering if installing the GTX 1050 or GTX 970 can boost the output significantly (maybe 2 or 3 times more ?). I am installing just as mentioned below. tar

[gmx-users] mpirun problem

Dear all, I am getting a problem with mpirun while I am trying to run the simulation using Gromacs.2018.4. However, it seems to work perfectly fine with the lower version of gromacs. The following is the error that I am receiving after the run: mpirun noticed that process rank 0 with PID 23603

Re: [gmx-users] Best force Field for Protein

Justn, >Then there are force fields that do better than others, but >the choice must be yours based on a thorough review of available >literature; Can you provide a list of FFs more suitable for folding and IDP simulations? Thank you, Dmytro From:

Re: [gmx-users] Average crystallographic angles for a triclinic box

Thanks, Justin, I was thinking the same about isotropic pressure. As we applying the same pressure from all directions, there would be only normal stress and imbalance in normal stress will manifest in the change in box length. Therefore the angles should not fluctuate. If what I am thinking is

[gmx-users] Adding an Oxygen into a Protein Heme Group; advice needed.

Dear all, I've stumbled across a problem with my input PDB files and I wonder if anyone could advise. For my structure, I need to add a carbonyl oxygen onto the axial position of the HEME group in my protein, which is connected to the protein backbone by a Fe-S bond to a Cysteine protein. I

Re: [gmx-users] Average crystallographic angles for a triclinic box

On 11/19/18 5:42 PM, Lakshman Ji Verma wrote: Hi all, I am trying to validate a force field (ff) for a crystal structure. I have done isotropic NPT simulations without restrains. I want to calculate the box length and angle (alpha, beta, gamma) to check the validity of the ff. I found one

Re: [gmx-users] Fatal Error: Atom N not found in building block 1DA . . .

On 11/19/18 3:50 PM, Austin Biaggne wrote: Hi All, I’m aware this issue has come up and been answered many times, but after reading through numerous threads regarding it and trying different solutions I am still having trouble finding a solution. I am trying to simulate a DNA strand (built

Re: [gmx-users] CHARMM36 GROMACS implementation

On 11/19/18 11:32 AM, John Whittaker wrote: Hi all, I am trying to reproduce the pure DPPC bilayer data found in J. Chem. Theory Comput., 2016, 12 (1), pp 405–413 (10.1021/acs.jctc.5b00935) using the recommended protocol given in the paper. Recently, I realized I made a mistake and have been

Re: [gmx-users] VMD visualization of clusters

On 11/19/18 8:57 AM, Rahma Dahmani wrote: Hi GMX users, After visualization of one of my clusters generated by g-cluster command in gromacs , i couldn't change the representation type in VMD from lines to new cartoon or secondary structure so i am wondering if this is related to the

Re: [gmx-users] Best force Field for Protein

On 11/18/18 10:46 AM, Edjan Silva wrote: Dear Gromacs users, I will perform a simulation of a protein with explicit solvent to verify structural changes in temperatures of 300 k and 310 k. I doubt any force field will give you any meaningful differences at such a small temperature

Re: [gmx-users] Residue id of capped peptide getting changed when adding molecules

On 11/15/18 12:39 AM, Dilip.H.N wrote: Hi, I have a capped peptide (ACE-ALA-NME) and now when i add the other molecules through the command "gmx insert-molecules", the residue id of the capped peptide, which was 1 as: 1ACECH3 1ACE HH31 1ACE HH32 1ACE HH33

[gmx-users] Average crystallographic angles for a triclinic box

Hi all, I am trying to validate a force field (ff) for a crystal structure. I have done isotropic NPT simulations without restrains. I want to calculate the box length and angle (alpha, beta, gamma) to check the validity of the ff. I found one similar thread but it doesn't answer my question.

[gmx-users] Fatal Error: Atom N not found in building block 1DA . . .

Hi All, I’m aware this issue has come up and been answered many times, but after reading through numerous threads regarding it and trying different solutions I am still having trouble finding a solution. I am trying to simulate a DNA strand (built using Chimera) by going through the same

[gmx-users] OPLS AA/M error

Hi all Gromacs Users, I wanted to conduct MD simulations using the newest OPLS-AA force field parameters - OPLS AA/M. I downloaded the folder with parameters from the main website of the developers and put it to the GMX top directory. The new ff is recognised, but while using pdb2gmx to create a

[gmx-users] CHARMM36 GROMACS implementation

Hi all, I am trying to reproduce the pure DPPC bilayer data found in J. Chem. Theory Comput., 2016, 12 (1), pp 405–413 (10.1021/acs.jctc.5b00935) using the recommended protocol given in the paper. Recently, I realized I made a mistake and have been using the CHARMM36 forcefield provided by Tom

Re: [gmx-users] Recovery simulation error (Bratin Kumar Das)

Thank you very much to all. Your indications helped me to continue and not lose the work done Em dom, 18 de nov de 2018 às 14:00, Edjan Silva escreveu: > to the end of the command you typed add: -deffnm cbd211_md > > > Em sáb, 17 de nov de 2018 às 08:00, > sys.kth.se> escreveu: > > > Send

Re: [gmx-users] generic hardware assembling for gromacs simulation

Seke, Yes, you can do a build with the components you have. The I5 ( 4760 ?) with 4 cores and no other threads is not particularly fast but should work The 1050 has some 640 or 768 cores depending on the version and will produce approximately a factor of 5x over the CPU alone. You will need at

Re: [gmx-users] VMD visualization of clusters

Hi Rahma, Have you tried any other visualization programs? Is there an example file one could try for visualization? Benson On 11/19/18 2:57 PM, Rahma Dahmani wrote: > Hi GMX users, > > After visualization of one of my clusters generated by g-cluster command in > gromacs , i couldn't change the

[gmx-users] VMD visualization of clusters

Hi GMX users, After visualization of one of my clusters generated by g-cluster command in gromacs , i couldn't change the representation type in VMD from lines to new cartoon or secondary structure so i am wondering if this is related to the structure of cluster ? ... why i can visualize the

Re: [gmx-users] generic hardware assembling for gromacs simulation

This should probably work. What operating system are you using? Are you using a later build of Gromacs, such as 2018.4 ? IF so have you tried the instructions here: http://manual.gromacs.org/documentation/current/install-guide/index.html Have you tried building an CUDA example programs? On

[gmx-users] generic hardware assembling for gromacs simulation

Dear Users. I apologise this this not exactly an GROMACs simulation question. I am a student and currently I trying to build a linux system for gromacs simulation. I have seen some materials about utilizing GPUs and multiprocessor but I can't fully understand some problems. I have a system