[gmx-users] Re: PMF calculation using g_wham using different simulation boxes

Li Jianguo ljgsq at yahoo.com
Thu Dec 3 04:19:54 CET 2009

Thank you Justin and Chris, for your comments and suggestions. 
All the restrained distances are less than half of the box length. The reason I want to use different box sizes is:  g_wham gives zero value for the first bin, so I need extend my simulation for long restrant distances for the use of -zprof0 option to make the PMF zero. Unfortunately, after finished simulations for short restraints, I realized that the box size may not be long enough for the use of -zprof0. Therefore I think of using larger box sizes for the rest of the windows with longer restraints. As you suggested, I need to do a test of finite-size effect before switching to larger box sizes.
Btw, for using g_wham, do I need to use the same parameters for different windows, e.g., the force constant, the simulation time and the width of the window?

Li Jianguo
Research fellow
Singapore-MIT Alliance
National University of Singapore

I have never heard of such a thing.  Is the restraint distance always less than 
1/2 the box dimension in the pulling direction?  If not, then this approach 
doesn't work.

I have always been under the impression that when running umbrella sampling, you 
have to actually be doing sampling in different regions of configurational space 
in the same system, in order to get a continuous energy function and appropriate 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


Message: 4
Date: Wed, 02 Dec 2009 08:42:36 -0500
From: chris.neale at utoronto.ca
Subject: [gmx-users] PMF calculation using g_wham using different
    simulation    boxes
To: gmx-users at gromacs.org
Message-ID: <20091202084236.bk7yqoke0w0wcwcs at webmail.utoronto.ca>
Content-Type: text/plain;    charset=ISO-8859-1;    DelSp="Yes";

Hi Li,

In my opiniun, what you propose is acceptable, but not rigorous, and  
you will need to prove that there are no unexpected artifacts of  
changing box size. For example, you should definitely run a couple of  
your small box systems as larger boxes as well and show that you get  
the same histograms for the distances between your polyatomic particles.

Justin is correct about the need for a box that is 2x larger than your  
displacement, and pull_pbcatom is an important option to set as well.


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