[gmx-users] RMSD truncation Restart simulation problems

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 10 19:23:07 CET 2011

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.


> Thanks,
> Henri
> On Tue, Mar 8, 2011 at 1:54 PM, Mark Abraham <Mark.Abraham at 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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