[gmx-users] decoupling two molecules as one group upon free energy calculation

[Justin Lemkul]

On 5/1/15 1:26 PM, V.V.Chaban wrote:
> Is there any handy way to decouple two molecules (defined as the same
> group or anyhow) upon free energy calculation?
>
> The case is applicable to ionic systems, for instance.
>
> =========================================
> If molecules for decoupling are submitted via an index file:
> Fatal error:
> Did not find any molecules of type 'A_B' for coupling"
>
> =========================================
> If molecules for decoupling are submitted as to groups: "couple-moltype = A B":
> Fatal error:
> Did not find any molecules of type 'A B' for coupling"
>

You can only couple a [moleculetype], not a group defined in an index file.  So 
the two molecules need to be merged into a single topological [moleculetype].

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================