Thanks for the help i will try this and check if the results point to some
issue.
I will get back as soon as i get some relevent information.
On Fri, Feb 23, 2018 at 11:59 PM, David A Case <david.case.rutgers.edu>
wrote:
> 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 Sat Feb 24 2018 - 06:00:03 PST
