sharada wrote:
Hello Justin,
Thanks for the reply . I apologise for the repeat mail. The parameters
are for ffG43a3 forcefield. Yes I am using the default electrotatics
cutoff values as an initial run. I would change to PME method as you
say. However I was wondering If r_epsilon value equals to 66 contributes
to a change in the simulation or this value holds good only if reaction
field is on ?
I have never heard of 43a3, do you mean 43a1, or perhaps 45a3? Better be sure
about what you're using so you get the .mdp options right. Use PME, and make
sure your values of rlist, rcoulomb, and rvdw are for use with that particular
parameter set (rvdw = 0.8 is particularly troubling, especially in the absence
of any dispersion correction).
With cut-off, the epsilon_r parameter is probably meaningless.
-Justin
sharada
*/-- Original Message --/*
From: "Justin A. Lemkul" <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Date: Sat, 31 Jan 2009 00:42:36 -0500
Subject: Re: [gmx-users] Melittin in methanol...
sharada wrote:
> rlist = 0.5
> rcoulomb = 1.4
> rvdw = 0.8
You are using cut-off electrostatics by default, so you are probably
getting
some bad artifacts (use PME instead). Also, the values of rlist,
rcoulomb, and
rvdw you are using do not correspond to those for which the Gromos96
force field
was derived. These make no sense. Refer to the original literature for
whichever parameter set you decided to use.
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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