From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Thu May 12 2005 - 13:24:10 CDT
Yes, indeed. I have written to him but I think the mail went only to
him. My answer was that f you are running a simulation with explicit
solvent, you don't need to set a dielectric constant different than 1.
The dielectric constant
is a property related to the collective polarizability of the
environment and will be automatically included in your calculation.
Indeed, it would be wrong to set it to a different value than the
vacuum dielectric constant.
On 5/12/05, Pijush Ghosh <pijush.ghosh_at_ndsu.edu> wrote:
> Hello all
> 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.
> Pijush Ghosh
> PhD Student
> Department of Civil Engineering
> North Dakota State University
> Fargo. ND. 58105. USA
> -----Original Message-----
> 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
> To: namd-l
> 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?
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