On Mon, Mar 07, 2016, Dan Roe wrote:
>
> Likely your trajectory files 'md_simulation9.mdcrd.gz' and
> 'md_simulation10.mdcrd.gz' have been either truncated or corrupted in
> some way. If they are truncated, cpptraj may have a better chance of
> reading the good frames if you first decompress (gunzip) the two
> trajectories. If the corruption has happened in the middle of one or
> both of the trajectories recovery of the data may not be possible. In
> the future I recommend that you use the NetCDF trajectory and restart
> formats (ioutfm=1 and ntxo=2 respectively) to avoid such issues.
>
> > I have performed 5 ns. I have run total 10 jobs, one job is equal to
> > o.5 ns. After 4 ns (md run = 9) my was killed. I started again.
Just to add to what Dan said: when you say you "started again", did you go
back to the end of run 8 and start over? If not, you probably need to do
that. (As Dan notes, you *may* be able to reconstruct some good frames, but
that is unlikely to be what you really want. You almost certainly want to
have a good trajectory for the whole 5 ns.)
....dac
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Received on Mon Mar 07 2016 - 09:00:06 PST
