[gmx-users] ensemble selection

Justin Lemkul jalemkul at vt.edu
Wed Sep 25 00:46:05 CEST 2013

On 9/24/13 2:40 PM, fatemeh ramezani wrote:
> Dear Justin
> I'm simulating gold nanoparticle interaction with protein by OPLSAA
> forcefield. I'm confused for selection an ensemble for my md run. I did
> energy minimization by NPT . then I did the MD by NVT. I did it because of

Let's take a step back.  EM is a non-dynamical process (there are no velocities) 
and thus does not belong to any sort of statistical mechanical ensemble. 
Therefore, EM is not done under NPT, NVT, NVE etc.

> studying of two paper that were similar to my project (Adsorption of
> histidine and histidine-containing peptides on Au(1 1 1):A molecular dynamics
> study by Zhen Xu, Shi-Ling Yuan and Interaction of b-Sheet Folds with a Gold
> Surface by Martin Hoefling, Susanna Monti, Stefano Corni).
> But in manual and tutorials of gromacs  is proposed energy minimization
> should be done by NVT and NPT and then MD should be done with NPT ensemble.
> in your idea should  I repeat my MD run by NPT ensemble? what is the
> difference of my result  between this two?

You need to eliminate the perception that manuals and tutorials dictate the only 
way that things "should be done."  These are merely suggestions for 
accomplishing a particular task.  What is true, however, is that you need to 
prepare and equilibrate the system such that it can be simulated under a 
relevant ensemble that models the experimental reality you wish to represent.  A 
protocol that follows: EM, NVT, NPT, and production is typically robust since it 
introduces temperature and pressure scaling sequentially, rather than all at 
once, which can lead to instability.

People often conduct simulations of biomolecules under NPT conditions because 
that's the ensemble present in a test tube in a lab or in the human body.  To 
understand the fundamental differences between partitioning functions, 
ensembles, free energies, etc between different ensembles, consult any 
statistical mechanics or molecular modeling book.  Just about all books on MM 
and MD feature some introductory material on these topics.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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