[gmx-users] couple-moltype

Mark Abraham mark.j.abraham at gmail.com
Sat Dec 9 07:33:12 CET 2017


You can only specify one moleculetype, but that entity can have more than
one molecule in it. So, make a salt pair moleculetype with at atoms section
that has the two ions you want, and make sure their coordinates are in
adjacent atom entries in the coordinate file in the right order for the
moleculetypes in your system in the usual way.

On Sat, Dec 9, 2017, 8:00 AM Jo <jojo412202 at gmail.com> wrote:

> Hello,
> I would like to use the 'free-energy' function in gromacs to perform the
> gradual insertion method to calculate chemical potential.  In doing so, I
> would like to use 'couple-moltype' to specify the molecule type of the
> molecule that I inserting.  However, I am inserting 2 molecule types (Na
> and Cl, defined as 2 molecule types).  Is there a way that I can tell
> gromacs to include both molecules insertions in the free energy
> calculation?  In the documentation, I could only find how to specify 1
> molecule for the calculation.
> Thank you,
> Jo
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