[gmx-users] pull code

Berk Hess gmx3 at hotmail.com
Tue Jun 8 14:40:45 CEST 2004

>From: acorrea at unisa.it
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: [gmx-users] pull code Date: Tue,  8 Jun 2004 13:07:00 +0200
>I just tried to performe PMF calucalition.
>I want to constraint the distance between only two
>atoms that are part of the same molecule for which no bonds are 
>Is it possible to constraint the distance between two atoms belonging to 
>same molecule and monitor the constrained force with pull code?
>I read on the manual VERSION 3.2 (page 118):
>"constraint force can be only be calculated between molecules or groups of
>molecules (..). If a constraint force is wanted between two atoms, this can 
>done through the free energy code."

It can be done with the pull code.
But I would prefer the free energy code, which can also be used with 

This point was quite unclear in the manual and I have updated it,
but it did not make it into the 3.2 manual release.

I have made an updated manual which you can obtain at:

This manual also explains how to use the free energy code for
calculating restraint and constraint forces.


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