Hi Chris,
I'm certainly no MMPBSA (or MMGBSA) expert, but I think the general
consensus is that it is better to have many short simulations (with
different starting velocities, and/or other differences) instead of one
long one, and long-ish MD simulations (>10 ns) don't have much benefit.
This may depend on the system of course!
See for example this paper (but there are more - just the first one I
found):
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029230/
Hope this helps,
Marc
On 3 May 2013 17:01, Chris Chris <alpharecept.yahoo.com> wrote:
> I am modeling the binding of a substrate to an active site and want to do
> some MMPBSA-derived binding energy calculations (MMPBSA-py-mpi).
>
> Looking in the literature- I see simulation times <1ns to 40 ns for
> production simulations. I have determined that my enzyme-substrate
> structures (there are 10) are stable from the equilibrations steps ( as
> outlined in Amber tutorial on mmpbsa).
>
> Is there any 'gold standard' for the length of production runs that yeild
> the most reliable mmpbsa energy outputs?
>
> Thanks,
> Chris
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 04 2013 - 04:30:02 PDT
