Re: [gmx-users] Continue simulation from the specific time

Thanks! 2013/5/29 Dr. Vitaly Chaban > If the frame was saved to the trajectory file, just extract it with > > trjconv -dump $timeframe -o conf.gro > > and continue your MD. > > No need for any additional energy minimizations, of course. > > Dr. Vitaly Chaban > > > > > > > On Wed, May 29, 2013 a

Re: [gmx-users] Continue simulation from the specific time

Aside from original question, you will probably want to initialize velocities (gen_vel) in order to evolve a different trajectory rather than repeating previous one. Dr. Vitaly Chaban On Wed, May 29, 2013 at 1:00 PM, Dr. Vitaly Chaban wrote: > If the frame was saved to the trajectory file,

Re: [gmx-users] Continue simulation from the specific time

If the frame was saved to the trajectory file, just extract it with trjconv -dump $timeframe -o conf.gro and continue your MD. No need for any additional energy minimizations, of course. Dr. Vitaly Chaban On Wed, May 29, 2013 at 12:45 PM, Андрей Гончар wrote: > Hello, I've got a questio

[gmx-users] Continue simulation from the specific time

Hello, I've got a question. Is there a way to continue MD simulation, not from last state but from specific time of MD? Say we have made a MD, have analysed it and have found an interresting molecule conformation at specific frame. Can we continue from this point or we should extract this frame, ma

Re: [gmx-users] Continue simulation

I got it now. Thanks. Happy TG! tpbconv -s md.tpr -extend 1 -o next.tpr mdrun -s next.tpr -cpi md.cpt Checkpoint file is from part 1, new output files will be suffixed part0002. Reading file next.tpr, VERSION 4.0.5 (single precision) Reading checkpoint file md.cpt generated: Tue Nov 24 15:00:12 2

Re: [gmx-users] Continue simulation

Jack Shultz wrote: Is it ok just to use tpbconv, even though we get this message "Continuation should be done by loading a checkpoint file with mdrun -cpi"? Please see the last paragraph in the "Version 4" section here: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations ++

Re: [gmx-users] Continue simulation

Jack Shultz wrote: Is it ok just to use tpbconv, even though we get this message "Continuation should be done by loading a checkpoint file with mdrun -cpi"? It depends on your objective, and you haven't told us enough about your .tpr and why your simulation stopped for us to know. See http://

[gmx-users] Continue simulation

Is it ok just to use tpbconv, even though we get this message "Continuation should be done by loading a checkpoint file with mdrun -cpi"? ++ I have tried mdrun using the -cpi flag mdrun -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md Then when I run the next u