VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Sun Feb 10 2008 - 16:10:36 CST

Thanks Peter :)

Michel

On Feb 10, 2008 3:55 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Michel,
> this dielectric constant works the same way as the NAMD dielectric
> constant; ie, it is considered a continuum dielectric throughout the
> *entire* system. There's no distinction between space occupied by solute
> and anything else. This is primarily intended for some of the cg models
> floating around the MDsphere; for almost any other simulation you'll be
> wanting to keep this at 1.0.
> Peter
>
>
> L. Michel Espinoza-Fonseca wrote:
> > Hi all,
> >
> > I'm using the NAMD energy plugin included in VMD 1.8.6. I noticed that
> > there is a new option in the GUI mode to set a dielectric constant.
> > However, it is not clear to me if that value corresponds to the solute
> > (in this case a protein or a peptide) or for the solvent. I assume is
> > for the latter. Your comments will be, as always, appreciated.
> >
> > Cheers,
> > Michel
> >
>