From: Pijush Ghosh (pijush.ghosh_at_ndsu.edu)
Date: Thu May 12 2005 - 12:53:32 CDT
I have a doubt in the line in which Dong asked this question,
When he is simulating his peptide in a water box (explicit water model),
isn't he already taking care of the dielectric? Does he still need to adjust
the dielectric constant to 80?
May be somebody can share some knowledge on this.
Department of Civil Engineering
North Dakota State University
Fargo. ND. 58105. USA
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Dong Luo
Sent: Thursday, May 12, 2005 11:53 AM
Subject: namd-l: dielectric constant
The default dielectric constant is 1.0 which means a
vacuum environment. I tried change it to 80 when I run
my peptide in water box with periodic boundary. The
single peptide chain soon turned to totally unfolded
after 9 frames (4.5ps). Is it reasonable or I can't do
Any suggestions on setting dielectric constant?
Do you Yahoo!?
Yahoo! Mail - You care about security. So do we.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:27 CST