Re: [AMBER] General question

From: Jason Swails <>
Date: Mon, 13 Aug 2012 22:08:01 -0400

On Mon, Aug 13, 2012 at 4:42 PM, George Tzotzos <> wrote:

> Hi everybody,
> I know that there is no prescribed answer to my question but I'd still
> like to ask as my computational power is rather limited (running a 24 core
> Mac)
> In calculating free energies of binding (MMPBSA) is it preferable to run a
> long trajectory or several smaller ones? I'm dealing with a proteins of
> ~150 residues.

Genheden et. al has discussed this point (DOI 10.1002/jcc.21366) and come
to the conclusion that several short simulations give rise to more
statistically converged answers, since you obtain more uncorrelated
structures that way.

Of course if you started with the same structure and ran only 10 fs, you
would get statistically converged answers as well (in that the standard
deviation would be small), since they're all effectively the same structure
(and you never know, the various snapshots may even appear uncorrelated :)
). That's obviously not what they did there (they ran ~200 ps per
simulation, IIRC), but I'm still not entirely convinced.


> Your experience is valued
> George
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Aug 13 2012 - 19:30:04 PDT
Custom Search