Re: last frame and restart are different

From: Francesco Oteri (
Date: Thu May 19 2011 - 15:50:06 CDT

Hi Jim,
1000 is multiple of 250 so the restart is written each four dcd frames.
Anyway, there are no frames matching with the restart. Moreover, log
file doesn't contain any error message!!!

The strange behaviour is that the restart configuration is a valid
structure. Usually when an error occur in coordinate generation, the
structure is distorted.
But this isn't the case.


Il 19/05/2011 21:02, Jim Phillips ha scritto:
> 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?
> -Jim
> 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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:18 CST