Hi,
Just to make sure I understand you correctly, the issue is that some
of the frames in your trajectory as written are corrupted (e.g. all
coordinates are 0.0 or something)? That usually indicates a problem
with the underlying filesystem (or network if it's over NFS) which is
something the software cannot correct.
However, skipping bad frames can be done automatically with cpptraj, e.g.:
trajin mytraj.nc
check skipbadframes <mask>
trajout fixed.nc
where <mask> selects your solute. If you're using the GitHub version
of cpptraj you probably don't even need the <mask> since the latest
version of the 'check' command is orders of magnitude faster.
Hope this helps,
-Dan
On Thu, Feb 8, 2018 at 7:39 PM, Ming Tang <m21.tang.qut.edu.au> wrote:
> Dear list,
>
> I ran an MD simulation in amber. Due to some reasons, the trajectories of hundreds of frames were not written, which affects some of my data analysis involving ‘average’ like RMSF. It is a headache to manually find out those frames and strip them one by one using trajin. Is there any better way for me to get a new trajectory which contains only frames whose trajectories are written?
>
> Any help is appreciated,
> Ming
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Feb 09 2018 - 06:00:05 PST
