Re: [gmx-users] Extending a simulation

2012-04-17 Thread Justin A. Lemkul
Shyno Mathew wrote: Dear all, This is the first time I am trying to extend a run in gromacs. I read in the gromacs website following are the steps to used for this purpose: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt So this means I don't

[gmx-users] Extending a simulation

2012-04-17 Thread Shyno Mathew
Dear all, This is the first time I am trying to extend a run in gromacs. I read in the gromacs website following are the steps to used for this purpose: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt So this means I don't need to modify the .mdp fi

Re: [gmx-users] extending a simulation after it get stopped because of queue time limit

2012-02-24 Thread Chandan Choudhury
On Sat, Feb 25, 2012 at 12:09 PM, priya thiyagarajan < priya.thiyagaraja...@gmail.com> wrote: > hello sir, > > i was performing simulation for 30ns. > due to queue time limit my mdrun stopped at 11.6ns.. then i extended my > simulation using these two commands > > *tpbconv -s md.tpr -extend 2

[gmx-users] extending a simulation after it get stopped because of queue time limit

2012-02-24 Thread priya thiyagarajan
hello sir, i was performing simulation for 30ns. due to queue time limit my mdrun stopped at 11.6ns.. then i extended my simulation using these two commands *tpbconv -s md.tpr -extend 2 -o newmd.tpr mdrun -s newmd.tpr -o md.trr -c md.gro -e md.edr -g md.log -cpi state.cpt -x traj.xtc -append

Re: [gmx-users] extending a simulation

2011-02-01 Thread Mark Abraham
On 1/02/2011 8:27 PM, Adwait Mevada wrote: Dear gmx-users, In order to extend my simulations, i am using grompp in the following fashion: grompp -np 8 -t amphiphilic_512dppc_50ns -c amphiphilic_512dppc_50ns -e amphiphilic_512dppc_50ns -f 850ns.mdp -p dppc.top -o amphiphilic_512dppc_900ns

[gmx-users] extending a simulation

2011-02-01 Thread Adwait Mevada
Dear gmx-users, In order to extend my simulations, i am using grompp in the following fashion: grompp -np 8 -t amphiphilic_512dppc_50ns -c amphiphilic_512dppc_50ns -e amphiphilic_512dppc_50ns -f 850ns.mdp -p dppc.top -o amphiphilic_512dppc_900ns followed by mdrun mpiexec -np 8 mdrun_mpi.o