On 6/03/2012 8:21 PM, Steven Neumann wrote:
Dear Gmx Users,
I am running my protein with ligand. at the begining of my simulation
the protein is far away from the ligand. Then in about 5-10 ns my
ligand binds to the protein surface remaining there for rest 90-95 ns.
Would you adjust coupling groups in thermostat as:
a) Protein_LIg and Water_and_ions
b) Protein Water_ions_LIG
c) Protein LIG Water_ions
I'd consider a single coupling group before any of those. See final part
of manual 3.4.8 and ref therein. c) is unsound because the ligand is
likely too small. The lack of T-group atom contiguity in a) might be an
issue, I'm not sure. b) is probably what people do, but you know this
from your literature searching about similar work, right? :-)
Mark
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