[gmx-users] Alchemically Change 1-4 Interactions

[Justin Lemkul]

On 6/2/15 2:07 PM, Eric Dybeck wrote:
> Hello All,
>
> I am attempting to alchemically change my solid small-molecule system from
> one forcefield to another using a series of linearly interpolated lambda
> states. For the bonds, angles, and dihedrals, a 'State A' and 'State B' can
> be specified in the topology file which will linearly change the parameters.
>
> However, my initial force-field has 1-4 interactions *included*, and my
> final force-field has 1-4 interactions *excluded*. How can I set this up
> within the topology file? Is there a way to have [ pairs ] change from
> state A to state B? Can I linearly change FudgeLJ and FudgeQQ? (The
> intermolecular interactions dont need to change, as they are the same for
> both force-fields).
>

You'll have to do some topology magic, probably.  The simplest thing to do 
(which I think will work) is to put the force field [defaults] directive under 
the control of an #ifdef block.  Then define lambda states in the .mdp (e.g. 
define = -DLAMBDA_0, -DLAMBDA_1, etc) and then the #ifdef blocks control which 
value of FudgeLJ and FudgeQQ are used.

Otherwise you'd have to manually specify pair parameters in [pairs] or 
re-calculate all the [pairtypes] for every intermediate state.

-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

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