VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Feb 10 2008 - 15:55:50 CST

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
>