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

From: Alejandro Gil Ley <>
Date: Thu, 11 Mar 2021 21:56:26 +0000

Thank you very much Prof. Roitberg and Prof. Case for your quick replies.
I appreciate you taking the time to reproduce this issue and providing such a detailed answer.


´╗┐On 2021-03-11, 1:18 PM, "David A Case" <> wrote:

    This email originated outside of Zymeworks

    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.)


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Received on Thu Mar 11 2021 - 14:00:02 PST
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