Hi,
I am trying to do an implicit solvent simulation using pmemd.cuda (I am
using amber16).
One question is, do I need to set a specific surface tension? Some MD
forums suggest that, but I did not find any reference to this in the sample
scripts given in the amber16 benchmarking page.
Another question is, is the GB solvent model related to the protein
parameters? I am asking because I am trying to use CHARMM parameters in my
simulation. I have done this in the past with explicit solvent simulations,
but I am not sure if the implicit solvent has to be "consistent" with the
force field parameters.
Regards,
Chitrak.
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Received on Fri Aug 05 2016 - 09:00:03 PDT
