[gmx-users] limitations in the umbrella sampling

[Seungho Choe]

Thanks a lot.
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RE: [gmx-users] limitations in the umbrella sampling

[Berk Hess]

From: Seungho Choe <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
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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[gmx-users] limitations in the umbrella sampling

[Seungho Choe]

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.



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