[gmx-users] Regarding Gromacs output files.

Hello Friends, I have two very specific queries regarding gromacs output files. 1) Since we can generate .xtc file during mdrun, Is is possible to stop generating .trr files, because it used to be very huge and less useful. 2) .xtc .tpr files generated by gms4.5.5 version is not readable by

Re: [gmx-users] Regarding Gromacs output files.

:17 AM, R.Vidya Rajendran (10PHD013) wrote: Hello Friends, I have two very specific queries regarding gromacs output files. 1) Since we can generate .xtc file during mdrun, Is is possible to stop generating .trr files, because it used to be very huge and less useful. Set nstxout, nstvout

[gmx-users] regarding g_covar

Hello Everybody, I am using g_covar with -xpmc flag in-oder to generate matrix of atomic correlation coefficients. At present I am using g_covar script given by Ran, which I downloaded from gromacs user modified script pool. Since Ran's script is for gromacs 3.3.3 and it not accept .trp input

[gmx-users] Regarding g_covar

Hello Everybody, I am using g_covar with -xpmc flag in-oder to generate matrix of atomic correlation coefficients. At present I am using g_covar script given by Ran, which I downloaded from gromacs user modified script pool. Since Ran's script is for gromacs 3.3.3 and it not accept .trp input

[gmx-users] Regarding g_cluster process MPI enabled

Dear Friends, Gromacs script such as g_cluster takes lot of time to complete in a single machine. Is their any way to give this job to a cluster machine like mdrun. Since mdrun is MPI enabled so I can easily execute it on cluster. Anybody in group have any clue that how we can execute g_cluster

[gmx-users] Selenomethionine in pdb file

Hello Friends, I would like to do simulation of a protein containing 'selenomethionine' [MSE] in coordinate file, during the first step of pdb2gmx this residue is not recognizing by any of the force field and getting fatal error 'Residue 'MSE' not found in residue topology database'. Please help

[gmx-users] concatenate md files

Dear Friends, I am doing simulation of a system containing a protein (T4 lysozyme L99A/M102Q) in complex with a ligand with the help of Justin tutorials. I ran following commands to perform production run (1000ps) grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_1.tpr