Dear All,
According to the on-line tutorial on Umbrella Sampling, there is a step to get
a lot of configurations, and for each configuration we need to run a MD. For
this reaon I regard the Umbrella Sampling method for binding energy calculation
is not suitable for relatively large protein complex (I am not sure the MW of
the complex used by Justin in the original publication. But for my
protein-ligand complex, the total MW is about 50, 000 Dalton), as for the MD
for all the configurations will take a rather long calculation time.
Do you agree on my view? Or do you have much better method?
Cheers,
Acoot
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: Acoot Brett <acootbr...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Sent: Tuesday, 3 April 2012 8:59 PM
Subject: Re: [gmx-users] on the Umbrella Sampling tutorial
Acoot Brett wrote:
>
> Dear All,
>
> For the on-line Umbrella Sampling tutorial
> "http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/04_EM_equil.html";
> of *Justin Lemkul*, will you pleasse tell me for the equilibration where
> there is no NVT equilibration?
>
It wasn't necessary. The system is quite robust and my experience has
indicated that NPT equilibration was sufficient.
-Justin
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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