[gmx-users] Constraints - PMF - Different Molecules

Mark Abraham Mark.Abraham at anu.edu.au
Sat Nov 15 15:48:26 CET 2008

Eudes Fileti wrote:
> Dear gmx-users, I need to use constraints between two
> polyatomic molecules in order to calculate PMF using free energy code.
> Can anybody help me to use these constraints over two different molecules?
> I ve already read something in the forum but not helped me enough.
> (see http://www.gromacs.org/pipermail/gmx-users/2006-February/020049.html).

In GROMACS usage, "constraints" are different from "restraints". I think 
the thread you referenced covers the issue reasonably - you need the 
relevant atoms to be in the same [ molecule ] section. That might mean 
two or more chemical molecules sharing a section.


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