[gmx-users] on the Umbrella Sampling tutorial

Acoot Brett acootbrett at yahoo.com
Wed Apr 4 03:16:43 CEST 2012

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?

 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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