From: Dmitry Mukha <>
Date: Tue, 13 Mar 2012 22:15:21 +0200

Ok, if x is a number of snapshots sufficient to get convergence for energy
of binding for system 1 and y is similar parameter for system 2, and x is
larger than y, you will be lucky to find an algorithm to make an estimation
of such a numbers in automatic fashion. Probably, you should take the
largest number of snapshots, x, multiplied on some coefficient larger than
1. Then, you can run your script for MMPBSA analysis for a set of your
compounds being sure that production run length won't be the reason of
wrong results. So, take as much as you can ))) (that is what I mean), both
for equilibration and for production. The reason for the largest error
still hides in wrong coordinates for protein-ligand complex, ff
parameterization and so on. The former can be overcome by long
equilibration if energy barriers are not too high.

2012/3/13 George Tzotzos <>

> Dear Dmitri,
> Many thanks for this. It makes sense to me, except for the last part
> "larger than optimal for individual case". What do you mean by this
> (individual case).
> Best regards
> George
> On Mar 13, 2012, at 8:19 PM, Dmitry Mukha wrote:
> _______________________________________________
> AMBER mailing list

Dmitry Mukha
Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
AMBER mailing list
Received on Tue Mar 13 2012 - 13:30:02 PDT
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