Re: Restart files are empy

From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Jul 22 2013 - 08:33:42 CDT

yes, the *.old files are just from the previous restart, so they should be
fine. Similarly, what you suggest about the trajectory will work.

On Sun, Jul 21, 2013 at 1:24 PM, Alessandro Mascioni <masci002_at_umn.edu>wrote:

> Hello,
>
> I have a question about restarting a simulation after a computer crash.
> For some reason my computer rebooted spontaneously.
>
> When I look at the restart files, they have a size of "0" and namd cannot
> open them:
>
> -rw-r--r-- 1 me me 38008708 Jul 21 09:44 protein.dcd
> -rw-r--r-- 1 me me 39736364 Jul 21 09:44 protein.dcd.BAK
> -rw-r--r-- 1 me me 0 Jul 21 09:44 protein.restart.coor
> -rw-r--r-- 1 me me 1727500 Jul 21 09:44 protein.restart.coor.old
> -rw-r--r-- 1 me me 0 Jul 21 09:44 protein.restart.vel
> -rw-r--r-- 1 me me 1727500 Jul 21 09:44 protein.restart.vel.old
> -rw-rw-r-- 1 me me 0 Jul 21 09:44 protein.restart.xsc
> -rw-rw-r-- 1 me me 241 Jul 21 09:44 protein.restart.xsc.old
> -rw-rw-r-- 1 me me 114068 Jul 21 09:44 protein.xst
>
> I assume the computer crashed before/during the restart files were
> updated. In this case should I restart from the .old files? Most of the
> configuration files I found on this mailing list do not restart from these
> .old files.
> When I use the .old files as restart condition namd seems to work fine.
>
> Also, for the firsttimestep, I used a script from this mailing list to
> determine the last timestep saved from the interrupted simulation.
>
> Should I set this timestep as firsttimestep and then cut the frames >= of
> this timestep from the old trajectory before merging the two trajectories?
>
> Thanks in advance,
>
> Al
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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