[gmx-users] couple-intramol

[Justin Lemkul]

On 1/3/17 2:40 PM, Qasim Pars wrote:
> Dear users,
>
> I got a little bit confused about the use of "couple-intramol". If I set it
> to "no", the intramolecular intractions of the ligand are "on" when the
> ligand is decoupled, right? It means that I don't need to set [

More specifically, intramolecular interactions are not a function of lambda; 
they are always in the A-state.  Only intermolecular interactions are modulated 
by lambda.

> nonbond_params ] part for the ligand?
>

You should never have to do anything with [nonbond_params] in these systems.

-Justin

> ; Free energy
> free-energy              = yes
> init-lambda              = 0
> delta-lambda             = 0
> sc-alpha                 = 0.5
> sc-power                 = 1
> sc-sigma                 = 0.3
> sc-coul                  = yes
> couple-moltype           = ligand
> couple-intramol          = no
> couple-lambda0           = vdw-q
> couple-lambda1           = none
> nstdhdl                  = 100
>
> Thanks in advance,
>

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

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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