On 4/04/2011 6:55 PM, Luca Bellucci wrote:
Dear all
I need to change sigma and epsilon for non-bonded parameters of the OPLSA FF.
In particular I want to set the attractive part of the LJ potential to zero
(C6=0).
In doing this I have read the manual but unfortunately the reported
explanation did not help me. To understand how it works in a reliable way,
I followed the Berk suggestions available at
http://lists.gromacs.org/pipermail/gmx-users/2010-December/056303.html
and i decided to report a simple example.
The main rules are in forcefield.itp file and for OPLSA FF they are:
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
The non-bonded force field parameters for two atoms are in ffnonbonded.itp
file and they look like:
[ atomtypes ]
; name bond_type mass charge ptype sigma epsilon
opls_1 C 6 12.01100 0.500 A sig_1 esp_1
opls_2 O 8 15.99940 -0.500 A sig_2 eps_2
From these values I am going to define the non-bonded parameter between a
couple of atoms as:
[ nonbond_params ]
i j func SIG_ij EPS_ij
opls_1 opls_2 1 (sig_1*sig2)^1/2 (eps_1*eps_2)^1/2 ; Normal behavior
However, if I want the attractive term C6 of LJ potential equal zero, I should
set sig_12=-sig_12
[ nonbond_params ]
i j func SIG_ij EPS_ij
opls_1 opls_2 1 -(sig_1*sig_2)^1/2 (eps_1*eps_2)^1/2 ; -sig_ij -> C6=0
It is right?
Yes, I think so. Set up a two-atom example to compare the normal and
modified functions. Get a trajectory frame, make energy group(s)
containing only pair(s) of atoms of interest and use mdrun -rerun to
compute the energy to your heart's content.
Mark
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