[gmx-users] Missing LJ interaction
fiedler at umich.edu
Sun Apr 1 19:32:36 CEST 2007
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.
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?
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