On Fri, Feb 23, 2018, Abhilash J wrote:
>
> I have a protein-2ATP complex. I ran the simulation using AMBER 14 for
> near about 200 ns in steps of 10 ns each. Now all of a sudden it does not
> start using the last rst file of last step. I had a look at the rst file it
> is complete and nothing else seems suspicious in it. I am able to make a
> valid pdb file ( without any stretching/banding of structure) using it. The
> out file also does not have any error. It simply writes the inputs used
> followed by results section. The section is empty of any results or error.
> How can i diagnose this issue. For now i have started the simulation back
> from 180 ns to see if it stalls again at 200 ns. But i have kept the old
> rst and out files for debugging.
Did you try a restart run with ntpr=1 (and a short nstlim)? This might give
you more information about what is going wrong. Ordinarily, on a restart,
Amber will not print anything until the first ntpr printout. So, setting
ntpr=1 has the potential for helping provide more info.
.....dac
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Received on Fri Feb 23 2018 - 10:30:02 PST
