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.
###################################################################################### 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 ###################################################################################### 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 ###################################################################################### Thank you very much. Yours sincerely Cheng -- 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://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.