[gmx-users] force field parameters for Fe3O4?

Dear gromacs users, I want to simulate a protein in different concentration of Fe3O4. How to obtain force field parameters of Fe3O4? Any help will highly be appreciated. Best, -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How to increase the volatile gpu-util

Dear gromacs users, I am running CG MD simulation on a Rocks cluster using the following command: gmx_mpi mdrun -nb gpu -v -deffnm gpu_md -ntomp 16 -gpu_id 0>& md.job & I tried the different value for the -ntomp option. With -ntomp 16 run will finish sooner than the other values for -ntomp. In

[gmx-users] volatile gpu-util

Dear gromacs users, I am running CG MD simulation on a Rocks cluster using the following command: gmx_mpi mdrun -nb gpu -v -deffnm gpu_md -ntomp 16 -gpu_id 0>& md.job & I tried the different value for the -ntomp option. With -ntomp 16 run will finish sooner than the other values for -ntomp. In

[gmx-users] problem: gromacs run on gpu

Dear Gromacs users, I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster system using command: gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on All things are ok. When I use this command in a script to do md simulation by queuing system:

[gmx-users] problem: gromacs run on gpu

*Dear Szilárd ,* *Thanx for your answer. * *For the following command, should I use -pin on?* gmx_mpi mdrun -nb gpu -v -deffnm gpu_md -ntomp 32 -gpu_id 0 Best wishes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] problem: gromacs run on gpu

*Dear Nikhil and Szilárd,* Thanks for your answers. I want to use only one of GPUs (for example ID =1). Should I use option -gpu_id 1? Information of my system hardware is as follows: Running on 1 node with total 96 cores, 192 logical cores, 3 compatible GPUs Hardware detected on host

[gmx-users] problem: gromacs run on gpu

Dear Gromacs users, I installed Gromacs 5.1.3. on GPU in Rocks cluster system. After using command: gmx_mpi mdrun -nb gpu -v -deffnm old_gpu, I encountered with: = GROMACS: gmx mdrun, VERSION 5.1.3 Executable:

[gmx-users] MD simulation of peptide amphiphile using CG method

Dear James, Thanks for your answer. As I understand, PyCGTOOL generates the coarse-grained molecular dynamics models from atomistic simulation trajectories. But, I don't want to do the atomistic simulation. Also, ATB only generates a complete topology for molecules containing < 40 atoms, while

[gmx-users] MD simulation of peptide amphiphile using CG method

Dear Peter, Thanks for your answer. > you'd best redirect this question to the Martini forum (cgmartini.nl), > since this is more of a forcefield question than a Gromacs question. You are right. At first, I asked my question in Martini forum, but no one didn't answer me. > look at the

[gmx-users] MD simulation of peptide amphiphile using CG method

Dear gromacs users, I want to do MD simulation of peptide amphiphile using CG method. My molecule is shown in the following link: https://ln.sync.com/dl/db2c92bf0#i8jm6yin-5uz4tn32-nq37ewxa-3vrkmt4b Can I use the default beads definition for my molecule (containing hydrocarbon chain and amino

[gmx-users] How to concatenate tpr files?

Dear Justin and Erik, Thanks for your answers. How to resolve my problem? How to obtain a reasonable RMSD curve from 10 consecutive MD runs? How to make an appropriate tpr for calculating RMSD? Best, -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How to concatenate tpr files?

Dear Justin, Thanks for your answer. > If you use gmx convert-tpr to simply change the number of steps > (much easier and cleaner!) Based on your suggestion, I used following command to extend first tpr to all steps. gmx convert-tpr -f final.xtc -s md1.tpr -n index.ndx -o new.tpr -extend

[gmx-users] How to concatenate tpr files?

Dear gromacs users, About the concatenation trajectory files, I have a question. I did 10 MD simulations (each section 10 ns). Now, I want to concatenate all of the trajectories and determine RMSD on whole trajectory. To do this, I used the following command: gmx trjcat -f md1.trr md2.trr

[gmx-users] g_mmpbsa

Dear gromacs users, Can I use g_mmpbsa tool for calculation of binding free energy in RNA-ligand complex? Best, Leila Karami -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http

[gmx-users] g_mmpbsa

Dear gromacs users, Can I use g_mmpbsa tool for calculation of binding free energy in RNA-ligand complex? Best, Leila Karami -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http

[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

Dear gromacs users I installed topolbuild version 1.3. I used following command line: ./topolbuild -n khob -dir ../dat/gromacs/ -ff gmx53a6.dat -meas I encountered with following error: Fatal error. Source code file: readmol2.c, line: 162 Atomic symbol O2 in atom type not found. How to

[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

my mol2file is as follows: @TRIPOSMOLECULE C:\Users\scc\Desktop\22.pdb 30 31 0 0 0 SMALL GASTEIGER @TRIPOSATOM 1 O2 0.99910.0511 -0.0859 O2 1 C1 -0.2444 2 C2 2.22660.0511 -0.0859 Car 1 C1 0.3522 3 N3 2.8760

[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

my mol2file is as follows: @TRIPOSMOLECULE C:\Users\scc\Desktop\22.pdb 30 31 0 0 0 SMALL GASTEIGER @TRIPOSATOM 1 O2 0.99910.0511 -0.0859 O2 1 C1 -0.2444 2 C2 2.22660.0511 -0.0859 Car 1 C1 0.3522 3 N3 2.8760

[gmx-users] constraint pulling

Dear Justin My system contains lipid + drug + water molecules. At first, I put drug molecule in middle of bilayer. Based on your tutorial, after minimization and equilibration, I generated configurations. After using distance.pl script, summary_distances.dat file is irregular such that no

[gmx-users] constraint pulling

Dear gromacs users I will use pull = constraint (constraint pulling) for PMF calculations. There is a tutorial about PMF from Justin in which he used pull = umbrella (umbrella sampling). In justin tutorial, step are as follows: 1) preparation of system 2) minimization equilibration 3)