From: Bachir Aoun (bachir.aoun_at_e-aoun.com)
Date: Sun Oct 06 2013 - 15:23:36 CDT
Dear NAMD users,
Is there any way to assign two different Lennard Jones (LJ) parameters to
the same atom type?
Explanation:
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
peaks positions.
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
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:45 CST