He, Yang wrote:
Hi Justin,
Thank you for your reply. In fact , for this base pair of "Gb2 Cb2 1
0.000194e10 0.00217e4", whatever I do , the final result for this base pair is
the same they will always separate from each other. Hence, I doubt whether this is
because gromacs did not read my force field file at all.
I hope to get your further suggestions about that.
What magnitude of values have you tried? Using 0.000194e10 (1.94e7) for epsilon
seems huge, but then, the only CG force field I've ever used is MARTINI (and
only with only a little experience). The magnitudes of sigma and epsilon for
that force field are on the order of e0, e-01, etc.
How are you determining your sigma and epsilon values?
-Justin
Thank you .
Yang
________________________________________
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL
PROTECTED]
Sent: Tuesday, November 25, 2008 3:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] course grain model for DNA
He, Yang wrote:
Hi all users,
when I am using the gromacs to simulate the course grain model for DNA, it
seems that the software doesn't recognize my force field file. I have included
all the bond and non-bond parameters in the bon.itp and nb.itp file.
During my simulation , I found that the base pair for C-G which first are in
the balance distance always repel from each other so I try to increase the
value of epsilon to increase the dispersion between this pair but it still did
not work and the pair still repelled from each other after the simulation .
Then I tried like this " ; Gb2 Cb2 1 0.000194e10 0.00217e4 " in
my nb.itp file, I found that the simulation can still be carried on and the simulation
result is the same for this base pair.
Well, that line is commented out (;), so naturally it would have no effect.
-Justin
So ,I got confused about this phenomenon . Can anyone of you give me some
suggestions?
Thank you in advance.
Yang
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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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--
========================================
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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