Henri Mone wrote:
Hi Mark,
Thanks for your feedback. The simulations are running now again.
I got one questions, I think it will be also of interest for the
others on the mailinglist.
I used "grompp" with the "-t state0.cpt" option, are the starting
velocities taken from the cpt files or are the assigned randomly from
a Boltzman distribution.
Meaning are the new simulations starting fresh or are they
acontinuation from the previous ones?
The grompp output should tell you. In older versions, when using a .trr file
(with velocities) for a restart, the combination of -t traj.trr and "gen_vel =
yes" caused the velocities in the .trr to be ignored and new ones generated. A
clear message was printed.
Check the screen output, and also compare the velocities in the .cpt with that
of your new .tpr files using gmxcheck/gmxdump.
-Justin
Thanks,
Henri
On Tue, Mar 8, 2011 at 1:54 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote:
On 8/03/2011 9:41 PM, Henri Mone wrote:
Ah yes, I remember now. mdrun tries to be smart and
check that all the files match the state they were in before
the crash by computing checksums when writing and again
when reading.
So the original problem was that the steps recorded in the different
.cpt are different, unsurprisingly.
To fix this, get the .mdp used to make the original .tpr, and call
grompp the same way, plus (e.g.) -t state0.cpt for each of the
replicas. Now the (matching) state information will be taken by
grompp from the (matching) checkpoint files, and no checksum
calculation can fail. Then
mdrun_mpi -multi 32 -replex 5000 -s new.tpr
should be fine (and no .cpt should be provided).
While doing this, I would avoid trying to use mdrun -append,
by the way. Glue things together later if you need to.
Mark
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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