Dear AMBER developers,
I am trying to run a TI simulation to calculate a solvation free energy
difference corresponding to the mutation of an amino acid side chain in a
protein. To do this I am running the TI calculation in water and also in
vacuo. I wanted to use pmemd because it is faster than sander, and so for
the in vacuo transformation I set igb = 6. However when I run the heating
at clambda = 0.5 in the gas-phase (but not in water) the temperature blows
up (no matter which thermostat I use). However this does not happen if I
change clambda to 0. Is this related to my having set igb to 6, and is it
possible to use pmemd for such a transformation in vacuo? If not, would it
be correct to use sander for the in vacuo transformation but use pmemd for
the solvated transformation?
Thanks,
Holly Freedman
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Received on Mon Feb 08 2021 - 10:00:02 PST
