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

From: Alejandro Gil Ley <alejandro.gilley.zymeworks.com>
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.

Thanks,
Alejandro


´╗┐On 2021-03-11, 1:18 PM, "David A Case" <david.case.rutgers.edu> 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.)

    ....dac


    _______________________________________________
    AMBER mailing list
    AMBER.ambermd.org
    https://protect2.fireeye.com/v1/url?k=7a8e5af1-251563f4-7a894f2c-86a279d0e4b2-1e0bfaf71b665eb3&q=1&e=fa12dc7c-98e4-488c-a0fb-f074fa3884bd&u=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber

Notice of Confidentiality: The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, re-transmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error please contact the sender immediately by return electronic transmission and then immediately delete this transmission including all attachments without copying, distributing or disclosing the same.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 11 2021 - 14:00:02 PST
Custom Search