On Tue, Jun 25, 2013 at 2:09 PM, <psu4.uic.edu> wrote:
> Dear Jason,
>
> Thanks. Wonder if the restart function will come in the next version of
> MMPBSA.py / AmberTools? Just curious.
This is unlikely. Checkpoints for these simulations would be incredibly
complex (especially in parallel!). Unlike MD or QM simulations, MM/PBSA
calculations are not well-ordered, so you can't simply store a single
restart file that captures the 'current' state in a checkpoint file. You
would need to figure out how many threads were running, how far _each_ one
had gotten in the 'last' calculation, redistribute the remaining work
across available threads, etc. Furthermore, normal mode calculations
currently performs the minimization and normal mode calculations in one
shot without printing any information (like minimized snapshots), so this
code would largely need to be rewritten to really make checkpoints
worthwhile.
Given that MM/PBSA calculations are intended to be 'quick' post-processing
analyses, the importance of having restart capabilities is somewhat
limited. These two factors provide a significant impetus to implementing
such functionality.
Sorry...
FWIW, I don't think you need anywhere near 100 frames for normal mode
calculations, especially since the structures are all minimized to the
nearest local minimum.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 25 2013 - 12:00:02 PDT
