[gmx-users] problem with append option while extending simulation

Dear All I'm running a simulation for 300 ns and I divided it into 6 production runs, each one for 50 ns using extending simulation commands: tpbconv_mpi -s run_50.tpr -extend 5 -o run1_50.tpr mpirun -np 48 mdrun_mpi -v -deffnm run1_50 -cpi run_50.cpt -append By using the -append option I e

Re: [gmx-users] Error: 'mdrun_mpi' is not a GROMACS command.

Hi, I'm using same command but without gmx_mpi and it works. On 18 Aug 2015 14:09, "anu chandra" wrote: > Dear Gromcas users, > > I just expericend an error while running mpi version of Gromcas on a 64 > processors in a cluster. The command I used for running mdrun is as > follows, > > mpirun -p

[gmx-users] Extending simulation with modifing .mdp file

Hi. I want to extend a simulation by 5 ps, but also I want to change some parameters in the old mdp file, so I type (run.mdp is the modified file) : grompp_mpi -f run.mdp -c run_50.tpr -o run1_50.tpr tpbconv_mpi -s run_50.tpr -extend 5 -o run1_50.tpr mpirun -np 60 mdrun_mpi -v -deffnm ru

Re: [gmx-users] High speed performance

Dr. Carsten Thank you so much :) On Tue, Aug 4, 2015 at 11:44 AM, Kutzner, Carsten wrote: > > > On 04 Aug 2015, at 00:02, Asmaa El khodary > wrote: > > > > Yes, I’m running the simulation on a cluster using 5 computational nodes, > In that case I would run on a sin

Re: [gmx-users] High speed performance

t two 10-core CPUs with HyperThreading = 2x20 > threads supported? > > -- > Szilárd > > On Mon, Aug 3, 2015 at 3:19 PM, Asmaa El khodary < > asma.moh_...@aucegypt.edu> > wrote: > > > Dr Carsten > > Thank you so much for your reply. Yes, you are right, it&#

Re: [gmx-users] High speed performance

Dr Carsten Thank you so much for your reply. Yes, you are right, it's a 40 core CPU. I'm using 2 fs time step with Particle Mesh Ewald for long-range electrostatics. I've attached the parameter file I'm using for the production run. Best Regards Asma On Mon, Aug 3, 2015

[gmx-users] High speed performance

Hi, I'm currently simulating a protein consists of 2776 atoms with 173 residues using CPU with 5 nodes, 40 core processors. The performance of the simulation is 70 ns per day (50 ns simulation takes almost 18 hours). Is this realistic or not? Thanks in Advance Asma -- Gromacs Users mailing list *

[gmx-users] Problem with gmx distance

Hi, I created an index files with two residue groups, 15 "r 22" contains 15 atoms and 16 "r 137" contains 24 atoms. Then, I use: gmx distance -s run.tpr -f run.xtc -n index.ndx -oall dist.xvg when I try to select both groups, I get this message Cannot match 'group "15"', because no such index group