[gmx-users] nonbond_params

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 26 16:31:23 CEST 2010

Amir Marcovitz wrote:
> Hi,
> 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 carbon)
> 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?

If you have already #included a force field file in the .top, it will have a 
[nonbond_params] section in it already.  You cannot add a new one.  The proper 
approach would be to modify the #included *nb.itp file.

> 2) Is [ nonbond params ] the right strategy to the task i described?

Sounds like one way to do it.


> Many Thanks,
> Amir


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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