**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Sun Oct 06 2013 - 15:36:22 CDT

**Next message:**Kenno Vanommeslaeghe: "Re: problem with Dihedral"**Previous message:**Bachir Aoun: "Lennard Jones (LJ) parameters"**In reply to:**Bachir Aoun: "Lennard Jones (LJ) parameters"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Look for the NBFIX section in the parameter file.

Axel.

--

Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0

International Centre for Theoretical Physics, Trieste. Italy.

-----Original Message-----

From: Bachir Aoun <bachir.aoun_at_e-aoun.com>

Sender: owner-namd-l_at_ks.uiuc.eduDate: Sun, 6 Oct 2013 15:23:36

To: <namd-l_at_ks.uiuc.edu>

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?

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

**Next message:**Kenno Vanommeslaeghe: "Re: problem with Dihedral"**Previous message:**Bachir Aoun: "Lennard Jones (LJ) parameters"**In reply to:**Bachir Aoun: "Lennard Jones (LJ) parameters"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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