[gmx-users] restarting a run using tpbconv
leafyoung at yahoo.com
Sat Jul 21 16:31:20 CEST 2007
The velocity is in the trr file. How many frames you have in
protein.trr? What's its last frame?
You also need to supply the energy file to tpbconv.
On 7/21/2007 10:15 PM, N-J.M. Macaluso wrote:
> This may be a trivial question, but how do you save velocities in this
> case? Would it be in the .mdp file or in the tpbconv command?
> Thanks for your help,
> On Jul 21 2007, David van der Spoel wrote:
>> N-J.M. Macaluso wrote:
>>> I am running a very long simulation, and the cluster I'm using
>>> has a wall time. I am using tpbconv to restart my simulations from a
>>> frame in the last run, but this doesn't seem to be working. When I
>>> analyze the second trajectory, the starting structure looks
>>> identical to the starting structure I had from the beginning. I am
>>> not sure if I am correctly using tpbconv.
>>> I'm taking the completed trajectory of the run I want to continue
>>> and start the second run from the 1300 ps frame:
>>> tpbconv -s protein.tpr -f protein.trr -o protein2.tpr -time -1300
>>> Then I submit the continued job with this command:
>>> mdrun -s protein2.tpr -o protein2.trr -c protein2.gro -g
>>> protein2.log -e protein2.edr -np 16
>>> Like I said, it doesn't seem to start the second run from the
>>> specified frame, but rather runs the simulation from the starting
>>> structure. I would appreciate any help.
>> you should save your velocities at regular intervals. it will start
>> from that last save velocities (t=0 in your case).
>>> Max Macaluso
>>> _______________________________________________ gmx-users mailing
>>> list gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users Please search the
>>> archive at http://www.gromacs.org/search before posting! Please
>>> don't post (un)subscribe requests to the list. Use the www interface
>>> or send it to gmx-users-request at gromacs.org. Can't post? Read
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users