[gmx-users] Missing LJ interaction

Steve Fiedler 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?
> Mark
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