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.
Mark
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