Project

General

Profile

Bug #2439

AWH deconvolution not working for sharing simulations

Added by Viveca Lindahl over 1 year ago. Updated over 1 year ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
mdrun
Target version:
Affected version - extra info:
GROMACS version: 2018.1-dev-20180306-33093601f
Affected version:
Difficulty:
uncategorized
Close

Description

The AWH PMF, extracted with gmx awh -s topol.tpr -f ener.edr -more, looks extremely "irregular" for awh-share-multisim=yes (see attached fig). When comparing to single-replica runs it's clear that this cannot be due to statistical noise. In this simulation there where 4 sharing simulations (-multidir walker-{1..4}).

awh-pmf-multi.png (34.2 KB) awh-pmf-multi.png Viveca Lindahl, 03/09/2018 09:42 PM
awh-share.tpr (313 KB) awh-share.tpr Viveca Lindahl, 03/09/2018 09:44 PM
md.log (33.5 KB) md.log Viveca Lindahl, 03/09/2018 09:46 PM

Associated revisions

Revision 229c8f63 (diff)
Added by Berk Hess over 1 year ago

Fix AWH deconvolution when sharing a bias

When sharing an AWH bias over multiple simulations, the PMF output
was garbage due to a missing minus sign in the reduction.
Note that this only affected the PMF output, not the sampling.

Fixes #2439

Change-Id: I688cda045f5e757e58b392d64384705b3ac73a17

Revision 22e00d62 (diff)
Added by Berk Hess over 1 year ago

Correct PMF sign error in AWH bias sharing

Recent commit 229c8f63 was though to fix a sign error in
the calculation of the deconvolution of the AWH PMF when sharing
the bias over multiple simulations, but this sign was misplaced.

Fixes #2439

Change-Id: I67ec06ff4d832a857467b58b362f9f6f88671aa8

History

#1 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related patchset '1' for Issue #2439.
Uploader: Berk Hess ()
Change-Id: gromacs~release-2018~I688cda045f5e757e58b392d64384705b3ac73a17
Gerrit URL: https://gerrit.gromacs.org/7666

#2 Updated by Berk Hess over 1 year ago

  • Status changed from New to Fix uploaded
  • Assignee set to Berk Hess
  • Target version set to 2018.1

It seems that a minus went missing during refactoring. We need a module test for bias sharing.

#3 Updated by Berk Hess over 1 year ago

  • Status changed from Fix uploaded to Resolved

#4 Updated by Mark Abraham over 1 year ago

  • Status changed from Resolved to Closed

#5 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related patchset '1' for Issue #2439.
Uploader: Berk Hess ()
Change-Id: gromacs~release-2018~I67ec06ff4d832a857467b58b362f9f6f88671aa8
Gerrit URL: https://gerrit.gromacs.org/7685

Also available in: Atom PDF