[gmx-users] couple-intramol

[Qasim Pars]

Hi,

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
>> 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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-- 
Qasim Pars