[gmx-users] Can I ask how to extend my simulations?

[Zhang, Cheng]

Dear GROMACS,

Can I ask how to extend my simulations? I would like to run a 50 ns job. Because of the cluster limitation, I need to use several jobs to complete that.


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Step1: grompp


After using "grompp" on my PC, I got the input file "md_0_1.tpr":


gmx grompp -f md.mdp -c npt.gro -t npt.cpt  -p topol.top -o md_0_1.tpr


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Step2: mdrun


As I see on

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

http://manual.gromacs.org/current/programs/gmx-mdrun.html


Can I ask if the following is correct in a job.sh file?

(Initially, "md_0_1.tpr" and "job.sh" are the only files in the folder.)


(I am still not sure how "-cpi", "-append", "-maxh" should be properly used. Do I also need to submit a second job with waiting dependency on the first job, what is the difference in the .sh file?)


(In the following, if 24 hours is assigned to each job, can I still get the .xtc file after the first job has finished?)


#!/bin/bash -l

#$ -S /bin/bash

#$ -l h_rt=24:00:0

#$ -l mem=4G

#$ -l tmpfs=15G

#$ -N MD

#$ -pe openmpi 24

#$ -cwd


module unload compilers

module unload mpi

module unload mkl

module load compilers/intel/13.0/028_cxx11

module load mpi/openmpi/1.6.5/intel.13.0-028_cxx11

module load atlas/3.10.1/intel.13.0-028_cxx11

module load fftw/3.3.4/double/intel.13.0-028_cxx11

module load gromacs/5.0/openmpi/intel.13.0-028_cxx11


gerun mdrun_mpi -deffnm md_0_1 -cpi -maxh 23



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Thank you very much.


Yours sincerely

Cheng