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
Mark Abraham wrote:
Steve Fiedler wrote:
Dear all,
I have encountered an unexpected behavior in which nonbonding values
for close intermolecular pairs do not appear to be always present. I
have reduced this problem to the configurational energy of two
triatomic isomers.
Everything looks OK to me - but you should check the results of diff
for your two topologies for unexpected differences. Does this happen
when you go from a single triatomic molecule to the diatomic?
Mark
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