[gmx-users] restarting mdrun

Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item#frames Timestep (ps) Step 1 Time

Re: [gmx-users] restarting mdrun

On 17/02/10 02:52, Chandan Choudhury wrote: Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item

Re: [gmx-users] restarting mdrun

Hi Mark !!! Thanks for answering. My query is how do I restart my mdrun because the command nohup mpirun -np 16 -machinefile mac mdrun -s md5-10.tpr -cpi state.cpt -append will not start from where the trajectory was stopped (i.e; time 9169.500). As this command will continue the simulation from

Re: [gmx-users] restarting mdrun

Chandan Choudhury wrote: Hi Mark !!! Thanks for answering. My query is how do I restart my mdrun because the command nohup mpirun -np 16 -machinefile mac mdrun -s md5-10.tpr -cpi state.cpt -append will not start from where the trajectory was stopped (i.e; time 9169.500). As this command

Re: [gmx-users] restarting mdrun

Thanks Justin !! But my state_prev.cpt file shows $gmxcheck -f state_prev.cpt Checking file state_prev.cpt # Atoms 186864 Last frame -1 time 9346.700 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces

Re: [gmx-users] restarting mdrun

On 17/02/10 04:43, Chandan Choudhury wrote: Thanks Justin !! But my state_prev.cpt file shows $gmxcheck -f state_prev.cpt Checking file state_prev.cpt # Atoms 186864 Last frame -1 time 9346.700 Item#frames Timestep (ps) Step 1 Time 1 Lambda

Re: [gmx-users] Restarting mdrun

Hi Chadan, I have used the two commands below to CONTINUE a run and they worked fine for me. I am also using gromacs-4.0.5. tpbconv -s wfullmdrun_extend2.tpr -extend 2000 -o wfullmdrun_extend3.tpr mdrun -s wfullmdrun_extend3.tpr -o wfullmdrun_traj.trr -e wfullmdrun_ener.edr -g md.log -cpi

Re: [gmx-users] restarting mdrun

Below is my .mdp file. The timestep dt shows as 0.001 ps title= protein cpp = /lib/cpp ; RUN CONTROL integrator = md nsteps = 300 dt = 0.001 ; NEIGHBOR SEARCHING nstlist = 10

Re: [gmx-users] Restarting mdrun

Thanks Lum !!! I had already used the suggestion you mentioned. But my problem is somewhat different. You can go through my previous mail, for more information. Thanks. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 11:42 PM, Lum Nforbi lumngwe...@gmail.com wrote:

Re: [gmx-users] restarting mdrun

On 17/02/10 04:43, Chandan Choudhury wrote: Thanks Justin !! But my state_prev.cpt file shows $gmxcheck -f state_prev.cpt Checking file state_prev.cpt # Atoms 186864 Last frame -1 time 9346.700 Item#frames Timestep (ps) Step 1 Time 1 Lambda