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

[Justin Lemkul]

On 5/24/15 11:57 AM, Zhang, Cheng wrote:
> 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
>

-cpi -append are used for any subsequent extensions, not the first run.  -cpi 
tells mdrun "start from an existing checkpoint, not time zero."  If there is no 
checkpoint, this is ignored.

-maxh was designed to work in concert with wallclock limits.  See the help text. 
  -maxh 24 is safe here since your limit is 24 hours.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================