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Message: 3
Date: Thu, 16 Apr 2009 14:11:51 +0200
From: Ran Friedman r.fried...@bioc.uzh.ch
Subject: Re: [gmx-users] the vdw and electrostatic energy
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 49e72087.8020...@bioc.uzh.ch
Content-Type: text/plain; charset=GB2312
Hi,
This problem has been discussed for decades in the literature. There are
approaches such as PME and reaction field to deal with the long-range
electrostatics.
I did not mean that. I want to know that when we use g_energy in
Gromacs to
read the energy from the file ener.edr, does the cutoff affect the values
of the energy? For example, when the cutoff is set to 1.2 nm and the PME method
is used, does the energy term Coul-SR read by g_energy contain the long range
part ?
Ran.
Dechang Li wrote:
Dear all,
When we do a MD simulation, we always set a cutoff
of non-bonded interactions, e.g. r=1.2 nm. When the
simulation finished, we can use the command
g_energy -f ener.edr -s ... to abtain the non-boned
energy of the system. My question is whether the non-bonded
energy values dependent on the non-bonded cutoff? If YES,
there may be no problem of the vdw interaction (LJ-SR),
because the vdw interaction vanish in a short distance. But
how about the electrostatic term with the distance dependence
of 1/r^2 ?
Best regards,
=
Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
P.R. China
Tel: +86-10-62773574(O)
Email: lidc02 at mails.tsinghua.edu.cn
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