From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Oct 06 2013 - 15:36:22 CDT
Look for the NBFIX section in the parameter file.
Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
From: Bachir Aoun <bachir.aoun_at_e-aoun.com>
Sender: owner-namd-l_at_ks.uiuc.eduDate: Sun, 6 Oct 2013 15:23:36
Subject: namd-l: Lennard Jones (LJ) parameters
Dear NAMD users,
Is there any way to assign two different Lennard Jones (LJ) parameters to
the same atom type?
I need to simulate an atomic system composed of 2 different atom types,
lets call those types A and B. There are no bonds and all the atoms are
neutral, therefore the only non-zero energy term is the lennard Jones one.
We already know from the experiment the distance distribution first shell
A-A = 2.5 Ang
A-B = 2.8 Ang
B-B = 4.5 Ang
The way lennard-Jones parameters are set in CHARMM ff is that every atom
type has its own Rmin as in the following expression
V(LJ) = Eps,i,j [ (Rmin,i,j / r,i,j)^12 - 2(Rmin,i,j / r,i,j)^6 ]
where: Rmin,i,j = Rmin,i / 2 + Rmin,j / 2
For the bi-atomic system described above we clearly need different LJ
parameters for A-A, A-B and B-B interactions !
Thanks in advance
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