[gmx-users] Missing LJ interaction
David van der Spoel
spoel at xray.bmc.uu.se
Sun Apr 1 20:00:10 CEST 2007
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.
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 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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