From: "Syma Khalid" <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users
<gmx-users@gromacs.org>
To: "'Discussion list for GROMACS users'" <gmx-users@gromacs.org>
Subject: [gmx-users] langevin dynamics
Date: Tue, 30 Oct 2007 16:55:59 -0000
Dear all,
I was wondering if someone could offer some advice?
I would like to run an atomistic langevin dynamics simulation (as I don't
want to include water explicitly). If I add the appropriate langevin
dynamics options in the mdp file, then is there any reason why I shouldn't
use explicit counter ions (unfortunately my protein has an overall charge)?
Obviously I would use periodic boundary conditions so the ions don't wander
off.
This question has come up many times on the mailing list
and I have answered in many times.
I will answer it once again.
Langevin dynamics is not a magic option that replaces your solvent.
Langevin dynamics only influences the dynamics, not the distributions.
If you choose a high friction, it might mimick the friction of water,
but it does nothing to your potentials.
Therefore you can not use Langevin dynamics will a normal protein
force field and just leave out the water. This will produce a vacuum
simulation.
Berk.
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