[gmx-users] free energy of removal of a molecule from the bulk

Justin Lemkul jalemkul at vt.edu
Sun Mar 23 23:43:37 CET 2014

On 3/23/14, 12:30 PM, Valentina wrote:
> I am running thermodynamic integration and I wanted to remove 1 molecule of
> water from bulk (as a test). But I am not sure how to specify it in the map
> file with couple-moltype:
> If I specify SOL I will be decoupling all of it, if I rename that specific
> molecule to something else, I get:
> The [molecules] section of your topology specifies more than one block of
> a [moleculetype] with a [settles] block. Only one such is allowed. If you
> are trying to partition your solvent into different *groups* (e.g. for
> freezing, T-coupling, etc.) then you are using the wrong approach. Index
> files specify groups. Otherwise, you may wish to change the least-used
> block of molecules with SETTLE constraints into 3 normal constraints.
> That is fair enough, but making index group and specifying the group r_570
> in the couple-moltype doesn't really work.
> Where am I going wrong?

You need to create a water topology that is basically the same as the rest of 
the waters, but with a special name and set of constraints.  You can't use 
multiple [settles] directives, so you need to specify a special water 
[moleculetype] with a name that is not SOL.  In it, you need to set 3 
constraints for O-H and H-H distances that mimic what [settles] is doing.  Then 
you should be able to treat this water molecule separately from the others.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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