[gmx-users] Explicitly defined nonbonded LJ pair terms?

Paul van Maaren maaren at home.nl
Sun Apr 10 17:46:12 CEST 2005

+++ Michael Shirts [Sat, Apr 09, 2005 at 12:42:09AM -0400]:
> 1. Does this work between atoms that are on _different_ molecules
> (i.e., alkane in water).

I think it should work.
> 2. When I try this  (inserting it just before the molecular
> definitions, and after all the type definitions, as so):
> [ nonbond_params ]
> ;   i       j    func     sig                              eps 
>  OW CT    1       0.332794606326    0.433634814359
>  OW HT    1       0.281262777488    0.2923565322
> I get the grompp error: Fatal error: Atomtype 'OW' not found!
> I'm unable to determine why this happen, as the atomtypes are defined
> earlier in the file.

This is too little info for me...
> 3. Apparently, these interactions are set up not to be perturbable by
> free energy.  Is this currently correct?  Any suggestion how I might
> want to compute using such a perturbative path (other than by writing
> the routines to do this)?    For methane, I can just change the C and
> H parameters -- for other molecules, this will be more difficult.



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