Hello all!
I am wondering if the solvate, genion, and energy minimization (using
steepest descent) procedures are deterministic. I have been performing
replicate energy minimization of a duplex DNA structure, always starting
from scratch (i.e., pdb2gmx) and using the same parameters in terms of
force field, water choice, ion concentration/type etc. and getting
convergent structures that are super-imposable. My question is whether
this is something that I would expect in any event, for any system (up
to energy minimization, before dynamics simulation), or that I just
happen to have a well-behaved system.
Thanks in advance,
Gregory
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