[gmx-users] restarting mdrun
Mark.Abraham at anu.edu.au
Wed Feb 17 00:58:10 CET 2010
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 1
> Coords 1
> Velocities 1
> Forces 0
> Box 1
> Here also the time is greater than the .trr file.
> Cant understand how to overcome it.
There's no reason any of this has to match.
The checkpoint file is written according to the interval supplied with
mdrun -cpt, default 15 minutes. The .trr file is written every so many
steps per the .mdp flags. So their contents will generally not match at
any point before the end of a run. They will match if it terminates
normally. Simlarly the filesystem timestamp that gets recorded can vary
with a whole pile of system variables, and need not match either. This
is all fine. Under GROMACS 4.x, the purpose of the .cpt is to facilitate
timely restarts without having to save excessive amounts of information
in the trajectory file. Instead you can just focus on storing the data
in your trajectory files that you need for your analysis. The website
pages talk more about this.
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