[gmx-users] Define custom moltype for free energy calculations

[Justin Lemkul]

On 1/27/16 9:50 AM, Tom Newport wrote:
> To give some background, I would like to be able to perform free energy
> calculations using a variety of different fairly complex selections to
> specify which bits of the system to turn on or off. These may include
> several proteins and several different ligands. There are other proteins
> and ligands which I do not want to include. This is for coarse-grained
> (martini) simulation of proteins and lipids, although I assume that doesn't
> make a difference.
>
> So, how is a moltype specified in GROMACS, and what is the least messy way
> of adding several molecules to one moltype? (or can this be specified more
> easily, say through using an index file?)
>

AFAIK, no, index files aren't useful here.  The free energy code works on 
anything defined as a [moleculetype], and only one at a time.  So you would have 
to merge whatever your molecules are into one [moleculetype] for this to work. 
That can be rather laborious to get everything hacked together and renumbered 
correctly.

-Justin

-- 
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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

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