From: Blake Charlebois (bdc_at_mie.utoronto.ca)
Date: Tue Nov 16 2004 - 15:06:50 CST
As I understand it, NAMD is not set up for implicit solvent simulations:
I think the dielectric constant for water is normally set much higher than
the solute (78.5 for water?, 2 to 20 for a protein?). I do not think NAMD
allows you to specify the dielectric constant in this way. However, there is
more to a good implicit solvent model than setting the dielectric constant.
Even then, there are disadvantages to any implicit solvent model.
To understand why NAMD requires dielectric constants greater than or equal
to 1, you would probably want to read up on the definitions of the
dielectric constant and electric susceptibility. I am not sure how a
material could have a dielectric constant less than 1. I vaguely remember
hearing someone arguing that it is possible.
Does anyone have anything to add?
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Ivan Vinogradov
Sent: November 10, 2004 11:17 AM
To: NAMD mailing list
Subject: namd-l: Implicit water dielectric constant.
does anyone knows what setting is appropriate in the configuration file
to implicitly include water in the simulation. I seem to recall a 0.67
value from somewhere, but in the NAMD manual is says that values
greater than 1 (the default) are required.
Regards, Ivan Vinogradov.
University of Toronto.
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