Dear All,
I am running a MD simulation (pmemd.CUDA, amber18) of a periodic box system
containing a protein, 500 ligand molecules (all the same) and water.
To avoid ligand aggregation during MD, I would like to define distance
restraints to keep the COM of the 500 ligands away (>5angst) from each
other. Considering that there are 500 ligands in the box, the &rst
definition appears difficult.
Has anybody defined restraints for similar purposes that are easier to
define?
Thanks a lot for the advice.
Regards,
giulio
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Received on Sun Dec 22 2019 - 08:30:02 PST
