[gmx-users] modify C6 directly in FF using sigma and epsilon

Mu Yuguang (Dr) YGMu at ntu.edu.sg
Fri Apr 6 03:25:55 CEST 2007

Dear David,
In fact I really did as you said. First prepare a top file which
explicitly include all bonded and nonbonded terms according to
combination rule. In this way that top file can be called stand-alone
top file (all the necessary parameters all included). Then you can do
what you want. In my case I modify 1,4 interaction.

Best regards
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive  Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of David Mobley
Sent: Friday, April 06, 2007 2:20 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] modify C6 directly in FF using sigma and epsilon

Gromacs users,

I'm using a force field (the port of AMBER to GROMACS) which uses
combination rules (combination rule 2), etc. in terms of sigma and
epsilon. However, I need to be able to modify C6 directly (in
particular, I want to be able to set it to zero). Can anyone give me
any pointers on a relatively straightforward way to do that? I want to
be able to continue using combination rule 2 but be able to separately
modify C6 for a couple atom types (or interacting atom pairs).

Obviously, one way I could work around this would be to explicitly
specify all of the nonbonded interaction pairs in my topology so that
the combination rules aren't used, then I could change the combination
rule so that I could modify C6 and C12. But since that would be a real
pain I'm hoping someone here can suggest something easier.

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