> After having "hacked" the topology file of my system,
> so that to have the protein (which is actually a dimer) and the ligand
> belonging to the same solute molecule,
If they were in the same molecule there (i.e. the dimer + ligand all in
the same molecule) then the periodic imaging would not be able to split
them assuming you are doing molecule based imaging (which is the default).
The only way for them to break would be actual disruption of the
structure.
You can send me off list the prmtop, mdin, short traj, and I can try to
figure it out... --tom
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Received on Wed May 30 2012 - 15:30:03 PDT
