[gmx-users] restarting mdrun

Mark Abraham 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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