[gmx-users] multiple nodes

Dear List, Below is the job script for running gromacs on our HPC (single node) #!/bin/bash -l #PBS -N gro1 #PBS -l walltime=300:00:00 #PBS -l select=3:ncpus=12:mpiprocs=12:mem=32gb #PBS -j oe cd $PBS_O_WORKDIR module purge module load gromacs/2019.3-foss-2019a export OMP_NUM_THREADS=12 gmx_mpi

[gmx-users] Equilibration using position restraints in NPT

Thank you Mark. The nanotube is 2x2x13 nm long. Then I use editconf with -c and -d 2 and solvate using spc216.gro. How can I calculate box size after NVT so that I get density of 1 or 0.99 when using pressure coupling? > Message: 1 > Date: Sun, 8 Oct 2017 23:38:58 +1000 > F

[gmx-users] Equilibration using position restraints in NPT

This is a very common post on previous mailing list however, I am still not able to fix the problem of position restraints during NPT. I have a carbon nanotube aligned to z-direction. I am trying to simulate infinite nanotube using periodic conditions. It is common to use position restraints for

[gmx-users] GROMACS 5.1.0 crashes on pbs queue system

Dear List, I have compiled gromacs 5.1.0 using MPI. The job runs interactively as well as through pbs submission using two nodes. However, the job crashes immediately when I submit more than two jobs. Below is the error: --

[gmx-users] GROMACS 5.1.2 performance

Dear list, I think the question on gromacs performance on cpu cluster has been raised many times in the mailing list. My apologies for reiterating the question. I am using a system ~8 atoms with virtual sites (hence timestep of 4 fs). The job hasn't completed yet but it seems that the jobs

[gmx-users] extending simulation

Dear List, I have only .xtc, .edr, .top and .tpr files. I want to extend my runs. I tried converting .xtc to .trr. Then I tried using both grompp and/or convert-tpr tools to extend my runs as recommended by gromacs manual. However, when I input new tpr file to mdrun it starts the run with time=0

[gmx-users] gromacs on multiple gpus

Dear List, I have compiled GROMACS 5.0.7 using following options CMAKE_PREFIX_PATH=/home/gandhin/fftw cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DGMX_MPI=on -DGMX_GPU=on -DGMX_SIMD=AVX2_256 -DCMAKE_C_COMPILER=${MPICCDIR}mpicc -DCMAKE_CXX_COMPILER=${MPICCDIR}mpicxx -DGMX_BUILD_MDRUN_ONLY=on

Re: [gmx-users] Carbohydrate GAG simulations

Hi Lara, I have worked extensively on GAGS in particular heparin. You may wish to refer to my publications. Glycam has residues for sulphated glucuronic acid/iduronic acid as well as sulphated glucosamine. You can build topologies for heparin using glycam webserver. If you wish to run your

[gmx-users] REMD exchange probabilities

Dear list, Using an exchange probability of 0.25 and temperature range 293-370 K, I calculated number of replicas using the server. However, when I did first run and tried exchanging replicas every 500 steps (1 ps), I don't think the exchange probabilities make sense in particular replicas 15

[gmx-users] centering molecule for movies

Hi List, I have simulated peptides in explicit water to form aggregate. I tried various options to post-process my trajectory (after removing water) using Gromacs 4.6.3 as described below. I want to record movie using VMD but the molecule translates and rotates during movie hence, I cannot

[gmx-users] Martini in Gromacs

Hello, I am trying to run coarse grained MD in gromacs. I get following errors, should I reduce the time step? Your feedback is appreciated. NOTE 1 [file prod1.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file prod1.mdp]:

[gmx-users] g_cluster

Hi List, I have come across mailing list where g_cluster can possibly be used for clustering of docked ligands. I tried g_cluster but it will change the reference coordinates with respect to the receptor. Is there a way to do clustering using g_cluster based on binding site? Many thanks, Neha

[gmx-users] counter ions in coarse grained simulations

Hi List, My query is not really related to gromacs but I appreciate response from people who might have tried using coarse grained simualtions using Martini force field in gromacs. I haven't come across tutorial or mailing list where people have added counter ions to a coarse grained protein

[gmx-users] gromacs bond restraints

How can I impose restraints in gromacs .mdp file or topology file to avoid isomerization of the peptide bond at the highest temperatures? Your help is appreciated -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia