[gmx-users] nonbond_params

Amir Marcovitz amarcovitz at gmail.com
Mon Jul 26 16:26:34 CEST 2010


my system is composed of two molecules, each is composed of a 36 carbon like
dummy atoms i defined in the amber files (i.e., has the LJ parameters of a
I'm interested in eliminating the attractive Lennard-Jones interactions
between the dummy atoms , such that only the repulsive terms will account.

I thought of adding a section to the *.top file:   [ nonbond params ] and to
set c6 to 0 such that the attractive term of the LJ is eliminated.
I used exactly the same syntax of the tutorial (page 98):

     * D     D        1       0.00000E-00       0.34252E-05*      ; (D is
just the name of my dummy atom)

but got a syntax error when running grompp:
*Fatal error:
Syntax error - File Surface_Surface_1.5_Sep_2.5.top, line 642
Last line read:
'[ nonbond_params ]'
Invalid order for directive nonbond_params*

1) what is wrong with my syntax? are there any further examples anywhere for
the usage of  [ nonbond params ] in topology files?
2) Is [ nonbond params ] the right strategy to the task i described?

Many Thanks,
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