[gmx-users] amide-capped C-terminus; OPLS force field

Dear all, Does anyone have any experience with capping C-terminal amino acid residues in the OPLS force field? What atomtypes should I use to maintain neutrality of the system? eg. If i have a cystine at the C-terminus residue, and I use the following atomtypes N opls_238 -0.5

[gmx-users] Two atom oscillational period less than the time step

Dear GMX users, Hello, I would like to discuss the grompp message that tells the bonded atoms oscillational period less than 10 times the time step. I am using 0.002 ps time step. The simulation was stopped because of LINCS warming. Is it need to decrease time step at least 10 times? Instead of

Re: [gmx-users] Gromacs 2019.4 - cudaStreamSynchronize failed issue

For the error: ``` ^Mstep 4400: timed with pme grid 96 96 60, coulomb cutoff 1.446: 467.9 M-cycles ^Mstep 4600: timed with pme grid 96 96 64, coulomb cutoff 1.372: 451.4 M-cycles /var/spool/slurmd/job2321134/slurm_script: line 44: 29866 Segmentation fault gmx mdrun -v -s $TPR -deffnm

Re: [gmx-users] Gromacs 2019.4 - cudaStreamSynchronize failed issue

Hi, What driver version is reported in the respective log files? Does the error persist if mdrun -notunepme is used? Mark On Mon., 2 Dec. 2019, 21:18 Chenou Zhang, wrote: > Hi Gromacs developers, > > I'm currently running gromacs 2019.4 on our university's HPC cluster. To > fully utilize the

[gmx-users] Gromacs 2019.4 - cudaStreamSynchronize failed issue

Hi Gromacs developers, I'm currently running gromacs 2019.4 on our university's HPC cluster. To fully utilize the GPU nodes, I followed notes on http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html. And here is the command I used for my runs. ``` gmx mdrun -v -s

Re: [gmx-users] toluene as a slovent

You also require a topology file for the toluene (.itp), include that in the system topology file (.top): *#include "toluene.itp" * Then add the molecule name and number of molecules added to the system to the molecule section at the end of the system topology file: [ molecules ]Toluene254

Re: [gmx-users] solvent evaporation modeling

Den 2019-12-02 kl. 00:03, skrev SAKO MIRZAIE: Hi All, I want to simulate a polymer: protein system in a way that water solvent will evaporated gradually. How should I do that? What parameters are needed to be included in the mdp file. Best Alexandra Patriksson, Erik Marklund and David van

Re: [gmx-users] solvent evaporation modeling

Dear André, Thank you very much for your email and hope Kalil has the script. Best regards On Mon, Dec 2, 2019 at 7:15 AM André Farias de Moura wrote: > Dear Sako, > > I'm ccing Kalil, who actually wrote and run the script to remove solvent > molecules, he might still have it. > > regards > >

[gmx-users] How to obtain the number of residue per turn with GROMACS ?

Hello, I would like to obtain the time serie of the number of residues per turn with GROMACS for a given peptide ? Is it possible to obtain this property with a GROMACS tool ? If yes, how ? Thank you Stéphane -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] toluene as a slovent

Den 2019-12-02 kl. 17:10, skrev Mijiddorj B: I recommend you to use (1) gmx insert-molecules tool to fill the box that solvent molecule. For the number of molecules, you can use as much as a higher number using -nmol option. The result tells you, how many molecules inserted from ordered numbers.

Re: [gmx-users] toluene as a slovent

I recommend you to use (1) gmx insert-molecules tool to fill the box that solvent molecule. For the number of molecules, you can use as much as a higher number using -nmol option. The result tells you, how many molecules inserted from ordered numbers. (2) Then, you should manually edit the

[gmx-users] energy minimisation error

Dear All, Good morning. I am doing the Protein Ligand complex simulation tutorial from the Gromacs website. I followed the tutorial without any issue. When I want to run the energy minimisation md, i get the error message Fatal error: grid cell cx -2147483648 cy -2147483648 out of range (max 24

[gmx-users] npt.tpr protein-lig

Good day, I have generated npt.tpr for my protein ligand and changed my npt.mdp file according to the suggestions by GROMACS for using Brendsen and h-bonds for constraints finally I encounter this NOTE which I think will cause further problems in my md run : NOTE 1 [file topol.top, line 18260]:

Re: [gmx-users] toluene as a slovent

Hello, I have downloaded the toluene pdb file and want to use it as solvent in GROMACS rather than the water molecules. I have added toluene as a molecule using gmx solvate -cs toluene.gro however, in the next steps, it is not added to the topol.top file and I cannot go-ahead to the next steps of