Thanks for the tips. The idea was to 'mimic' the interior of a lipid
bilayer where the dielectric constant is low comparatively to the value for
water.
- Jose
On Wed, Dec 7, 2011 at 1:17 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I think the combination of the igb=7 model (with appropriate radii) and the
> ff99SB force field performs well for use of GB as a water model- but I
> think there is little experience with GB as an implicit low dielectric
> solvent. likewise, the peptide force fields themselves are really designed
> for aqueous solvent.
>
>
> On Wed, Dec 7, 2011 at 11:43 AM, Jose Borreguero <borreguero.gmail.com
> >wrote:
>
> > Dear AMBER users,
> >
> > I've never used an implicit solvent force field, I wonder which one is
> the
> > most adequate to simulate a peptide in an implicit solvent with low
> > dielectric constant. Also, how do I set the value of the dielectric
> > constant in the simulation?
> >
> > - Jose
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 07 2011 - 11:30:02 PST
