[gmx-users] Re: meaning of the parameters in gbsa.itp

[Corina Mo]

Dear Justin,

Thanks again! Will look into it.
Btw, you know if there is any plan to implement implicit lipid model in
GROMACS?

Corina


On Fri, Oct 25, 2013 at 12:17 AM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5011968h67 at n6.nabble.com> wrote:

>
>
> On 10/24/13 12:11 PM, Coco Mo wrote:
> > Thanks Justin for the quick hint!
> > So, only the last two columns are needed. Sorry for the stupid question,
> > where can I obtain reliable values for the atomic van der waals radii?
> Is
> > it I have to calculate from the original force field parameters, in my
> > case, the opls?
> >
>
> Four of the atom types you cite are carbon.  Note how the radius values
> barely
> change between different carbon types.  I would first start by assigning
> the
> parameters from something chemically similar.  The fluorine atom is more
> tricky,
> not so much in assigning the radius, but in assigning the scaling factor.
> You'll have to look for advice not from the OPLS force field papers, but
> from
> the GBSA algorithm you will be using.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
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-----
Thanks.

Corina 
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