[gmx-users] Two [ defaults ] sections

[Justin Lemkul]

On 5/6/16 1:12 PM, Alexander Alexander wrote:
> Dear gromacs user,
>
> I have a system containing a "peptide+water+solid surface", for the
> "peptide+water" I hired the OPLS-AA force field which has below [ defaults
> ] section in its "oplsaa.ff/forcefield.itp"
>
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>        1                3                    yes                0.5
> 0.5
>
> While I would like to specify the below [ defaults ] section in for the
> solid surface.
>
> [ defaults ]
> ;  nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>        1                 3                    no                0.5
> 0.5
>
> Here the only different between the two [ defaults ] section is just
> "gen-pairs" (that I do not know how big would be the side effect if I just
> used the one for OPLS-AA force for the whole new system containing solid
> surface as well?!)
>

The function of gen-pairs is described in the manual.

> But in general, I would be highly appreciated if you let me know how I can
> have two different [ defaults ] sections in my final "peptide+water+solid
> surface" system.
>

You can't.  [ defaults ] can only ever be present once, because it provides the 
instructions for the functional form.

-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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