[gmx-users] Missing LJ interaction

[David van der Spoel]

Steve Fiedler wrote:
> Thank you for looking over the input and for suggestions Mark.  
> Unfortunately, a comparison of the topologies with diff revealed no 
> inconsistencies.  GROMACS can correctly recognize the presence of the 
> significant repulsion (e+10) between atoms 1 and 5 when the atoms from 
> both triatomic molecules are incorporated into a single molecule.
> 
> I have found one clue in that the missing repulsion in the bimolecular 
> system, can be returned by increasing rlist >= 0.77 nm in grompp.mdp.  
> This is unsatisfying, as the distance between atoms 1 and 5 is much 
> shorter, 0.057 nm.  As these coordinates were taken from a calculation 
> of membrane system just before a crash, I believe it is this lack of 
> intermolecular nonbonding repulsion responsible for allowing atoms 1 and 
> 5 to get this close in the first place.
> 
> Again, any insights are most welcome.
> 
> Steve

I didn't follow the thread but it is the distance between charge groups 
that determines whether interactions are incorporated in the 
neighborlist. Check the manual about charge groups.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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