From: Seungho Choe <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: gmx-users@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.
Berk.
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