[gmx-users] limitations in the umbrella sampling

Berk Hess gmx3 at hotmail.com
Wed Mar 7 16:08:19 CET 2007

>From: Seungho Choe <choesh at umich.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] limitations in the umbrella sampling
>Date: Tue, 06 Mar 2007 17:33:38 -0500
>Dear all,
>In the manual, it says :
>If a group contains part of a molecule of which the bondlengths are 
>constrained, the results may be unreliable.
>I'm a little confused.
>Let's think of the following two cases (A: the reference group, B: a group 
>which will be pulled) :
>1) A(partially constrained)  + B (no constraints)
>2) A(no constraints) + B(partially constrained)
>Does it mean that both pmf calculations are not reliable ? Should I use the 
>free energy code for both cases ?
>Any comments would be appreciated.
>Thank you.

If you read the manual more carefully you can see that this
restriction only applies to constraint pulling, not umbrella pulling.


Live Search, for accurate results! http://www.live.nl

More information about the gromacs.org_gmx-users mailing list