On Thu, Mar 11, 2021, Adrian Roitberg wrote:
>> After the first initial steps using steepest descent, CG energies and
>> forces exhibited frequent jumps of several orders of magnitude as the
>> minimization progressed.
But it looks like you are still getting lower energies.
FWIW: the conjugate gradient code in runmin is about the oldest code
around in Amber: I think it even precedes molecular dynamics. The entire
runmin subroutine will be gone from future releases of sander, but not for
AmberTools21. I don't know how we will handle the situation for pmemd.cuda.
>> If the xmin minimizer is used with PRCG then the issue disappears.
Indeed. Anyone who wants a good minimization should use xmin; just be sure
to turn off SHAKE. (The latter is done automatically in development codes.)
....dac
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Received on Thu Mar 11 2021 - 13:30:02 PST
