On Tue, Jun 18, 2013 at 2:23 PM, Aditya Padhi <adi.uoh.gmail.com> wrote:
> Hi Jason,
> Thanks for the quick reply and the suggestion about the cutoff. But I
> would like to bring to your attention that I have a simple protein
> (basically a single protein, not a complex). Although I tried to run the
> simulation with a higher cut-off as you suggested, the error massage is
> again the same that I posted in my previous mail and eDo you have ventually
> the job stops. Do you have any comment on this? Shall I modify or do some
> additional stuffs here?
> I would be really grateful if you can help me in this regard.
>
What happens when you visualize the trajectory? This is typically the best
'first' step in debugging these types of problems. Perhaps your system
started out with some initial momentum? Try and see if you can tell why
particles would be moving so far away. If you can't tell, then I would
suggest printing snapshots more frequently in case you missed what
happened...
There are too many potential causes to settle on one using the information
you provided. I've also never done ALPB simulations before (and it is less
popular, to my knowledge), so there might be something happening with that,
too (although it's just a rather simple modification of the GB potential).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jun 18 2013 - 12:30:02 PDT
