[gmx-users] How to run MD simulation remotely

[Erik Marklund]

Dear Charles,

Is mdrun_mpi available on the node side? Nothing in the script suggests it is, but sometimes part of the environment is inherited from the session where sub was run. Do you get any output files at all? I would expect the stdout and stderr to provide some error message.

Kind regards,
Erik

> On 9 Jul 2016, at 10:55, charles k.davis <charles_p140045bt at nitc.ac.in> wrote:
> 
> Dear all,
> 
> My name is Charles, PhD student at National Institute of Technology,
> Calicut, India.
> 
> I'm facing problem in giving Gromacs MD simulation job remotely (via ssh
> command) in a Hybrid Cluster system. The system administrator told me to
> copy paste the following script
> 
> *#! /bin/bash *
> *#PBS - q small *
> *#PBS -e errorfile.err *
> *#PBS -o logfile.log *
> *#PBS -l select=2:ncpus=16  *
> *tpdir=`echo $PBS_JOBID | cut -f 1 -d .` *
> *tempdir=/scratch/job$tpdir *
> *mkdir -p $tempdir *
> *cd $tempdir *
> *cp -R $PBS_O_WORKDIR/* . *
> *mpirun -np 32 -hostfile $PBS_NODEFILE mdrun_mpi -v -s input.tpr -c
> output.gro*
> *mv ../job$tpdir $PBS_O_WORKDIR/.*
> 
> 
> in a text document and save it as* script.sh* and to submit the job run the
> following command in terminal,
> 
> 
> 
> *qsub script.sh*
> This method is not working for us. It will show that the job has been taken
> up but soon it will vanish.
> 
> In our lab workstation (which we control directly, not remotely) we use the
> following commands lines,
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> *pdb2gmx -f Protein.pdb -o Protein.gro -p Protein.top -water spc
> -ignhgenrestr -f UNK.gro -o posre_UNK.itp -fc 1000 1000 1000grompp -v -f
> minim.mdp -c Protein.gro -p Protein.top -o Protein-EM-vacuum.tprmdrun -v
> -deffnm Protein-EM-vacuum -c Protein_minimized.gro -nt 1editconf -f
> Protein_minimized.gro -o Protein_minimized_box.gro -d 1.1 -bt cubicgenbox
> -cp Protein_minimized_box.gro -cs spc216.gro -p Protein.top -o
> Protein-water.grogrompp -v -f minim_water.mdp -c Protein-water.gro -p
> Protein.top -o Protein-water.tprgenion -s Protein-water.tpr -o
> Protein-water-ions.gro -p Protein.top -conc 0.15 -neutral -pname NA -nname
> CLgrompp -v -f minim_water.mdp -c Protein-water-ions.gro -p Protein.top -o
> Protein-EM-solvated.tprmdrun -v -deffnm Protein-EM-solvated -o
> Protein_minim_traj_water.trr -c Protein_minimized_water.gro -e
> minim_ener_water.edrmake_ndx -f Protein_minimized_water.gro -o
> index.ndxgrompp -v -f nvt.mdp -c Protein_minimized_water.gro -p Protein.top
> -o nvt.tprmdrun -v -deffnm nvtgrompp -f npt.mdp -c nvt.gro -t nvt.cpt -p
> Protein.top -o npt.tpr -n index.ndx mdrun -v -deffnm nptgrompp -f md.mdp -c
> npt.gro -t npt.cpt -p Protein.top -o Protein_md_1.tpr -n index.ndx mdrun -v
> -deffnm Protein_md_1*
> 
> to do the simulation and keeping the files md.mdp, minim.mdp,
> minim_water.mdp, npt.mdp and nvt.mdp in the work directory. We also keep
> protein file as Protein.pdb and ligand file as UNK.pdb, UNK.gro and UNK.itp.
> 
> Can someone help me sort out this problem.
> 
> Many thanks,
> 
> Regards,
> 
> Charles K Davis
> PhD Student
> School of Biotechnology,
> National Institute of Technology,
> Calicut, Kerala, India-673 601
> Cell Phone: +91 9495595458
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