Re: last frame and restart are different

From: Jim Phillips (
Date: Thu May 19 2011 - 14:02:25 CDT

If you're writing dcd every 250 steps and restart every 1000 then I would
guess there are several steps in the dcd file after the restart. These
are all recorded in the log file. Do any of the last four dcd frames
match the restart file?


On Thu, 19 May 2011, Francesco Oteri wrote:

> Dear namd users,
> I've simulated a protein in multiple-run and now I'm concatenating the
> resulting chunks to have the complete trajectory.
> I've noticed that in a particular chunk (say i-th) the last frame of the DCD
> trajectory and the restart coordinates are different (RMSD = 3A).
> As a result the (i+1)th chunk is started from different position and now I
> have a discontinous trajectory.
> The trajectory has been produced using 2.7b3 version and it is 175000 steps
> long, coordinates are saved every 250steps and restart file is saved every
> 1000steps.
> My questions is: is there anybody who experienced the same problem? How can
> I solve it?
> Regards

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