Re: [AMBER] Problem with CG minimization in implicit solvent

From: Chris Neale <>
Date: Thu, 11 Mar 2021 21:33:37 -0700

Wild guess: does this code increase the step size without bound every time
an iteration leads to a lower energy? If so, limiting the max step size
could be a solution as I've seen this type of algorithm (even in steepest
descent) lead to pathologies in energy minimization of systems that start
far enough from a minimum that the step size becomes unwieldy large at some

On Thu, Mar 11, 2021 at 2:18 PM David A Case <> wrote:

> 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 - 21:00:02 PST
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