Grace Tang wrote:
Sorry, I wasn't too clear in the first message. I will be using OpenMM
Gromacs, which does support implicit solvent.
My current energy minimization steps only lower the energy to -5E3. Is
this okay considering water is not around?
Probably.
Is is necessary to do equilibration if I am using implicit solvent?
Yes. Generated velocities on an arbitrary starting structure will not
necessarily be in the correct thermodynamic ensemble.
> Is
so, can anyone direct me to reasonable parameters?
Parameters for what? You should be looking closely at the documentation
for OpenMM, and the methods in whatever publications they may have made
using it. If they haven't published, and you aren't in close contact
with them, then you should reconsider your choice of software. The kind
of science you want to do should usually drive that choice.
Mark
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