qasimpars at gmail.com
Wed Jan 4 06:10:40 CET 2017
Thanks. If I want to calculate the intramolecular energy of the ligand, I
need to choose Coul-14:LIG-LIG, LJ-14:LIG-LIG, Coul-SR:LIG-LIG and
LJ-SR:LIG-LIG in the .edr file. Am I wrong?
On 4 January 2017 at 04:03, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
> ; 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
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