[gmx-users] Problem with gromacs in Cluster

Hey all, I recently ran 20ns simulation of protein ligand complex on cluster i used following script to run simulation grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_test.tpr mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8 *I saved this as MD.sh And then submited

Re: [gmx-users] Problem with gromacs in Cluster

On 4/25/13 8:28 AM, Sainitin Donakonda wrote: Hey all, I recently ran 20ns simulation of protein ligand complex on cluster i used following script to run simulation grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_test.tpr mpirun -n 8 mdrun -s md_test.tpr -deffnm

Re: [gmx-users] Problem with gromacs in Cluster

You can split the simulation in different part (for example 5 ns each), every time you'll finish one you will extend it adding more time. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend My cluster uses a different script system than yours so I can't help with

Re: [gmx-users] Problem with gromacs in Cluster

I generally build a tpr for the whole simulation then submit one job using a command such as: mpirun -n ${NUM_PROCESSORS} mdrun -deffnm ${NAME} -maxh ${WALL_TIME_IN_HOURS} copy all the files back at the end of the script if necessary then: then resubmit it (sending out all the files again

Re: [gmx-users] Problem with gromacs in Cluster

The salvation is to use: mdrun -cpi state.cpt Dr. Vitaly Chaban On Thu, Apr 25, 2013 at 2:37 PM, Justin Lemkul jalem...@vt.edu wrote: Can any body tell me how do it split script i such that i will get all 20ns simulation You specified a given time limit for the job, and the run

Re: [gmx-users] Problem with gromacs in Cluster

This works well until you use a system that permits job suspension. Then -maxh gets double-crossed... :-) Mark On Apr 25, 2013 3:41 PM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: I generally build a tpr for the whole simulation then submit one job using a command such as: