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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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