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Bug #2640

coul-lambda affects the pressure computation of a ligand with zero partial charge

Added by zhiyi wu over 1 year ago. Updated about 1 year ago.

Status:
Closed
Priority:
High
Assignee:
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

This is a simplified and corrected version of the issue 2600.
I'm trying to compute the decoupling free energy of vdw interactions of a ligand which has zero partial changes.
Since the ligand has zero partial, changing coul-lambda shouldn't have any effect on anything.
However, setting coul-lambda to 0 yields a pressure 2.13121e+02 bar of whereas setting coul-lambda to 1 yeilds a pressure of 1.07168e+02 bar.
The commands to reproduce the results are
gmx grompp -f coul-lambdas_0.mdp -c prod.gro -o coul-lambdas_0.tpr
gmx mdrun -deffnm coul-lambdas_0 -rerun prod.gro
gmx grompp -f coul-lambdas_1.mdp -c prod.gro -o coul-lambdas_1.tpr
gmx mdrun -deffnm coul-lambdas_1 -rerun prod.gro

If you compare the pressure in coul-lambdas_1.edr and coul-lambdas_0.edr, you will notice that the pressure are different whereas they should be the same.

pressure.tgz (6.16 MB) pressure.tgz zhiyi wu, 09/07/2018 02:54 PM

Related issues

Related to GROMACS - Bug #2849: Free energy discrepancies between GROMACS versionsClosed

Associated revisions

Revision 12f01f79 (diff)
Added by Berk Hess over 1 year ago

Fix PME forces with FE without perturbed q/LJ

PME would incorrectly scale the mesh forces with lambda when no
charges or LJ atom types were actually perturbed.

Fixes #2640

Change-Id: I193d55cf76d842f5b04d3a220411282c06b08a90

History

#1 Updated by Berk Hess over 1 year ago

  • Category set to mdrun
  • Status changed from New to Accepted
  • Target version set to 2018.4

I reproduced this issue.
Also the force on non-perturbed, charged atoms differ significantly with coul-lambda, even though the Coulomb energies do not.

#2 Updated by Berk Hess over 1 year ago

The issue disappears when not using LJ-PME. So this looks like some incorrect interaction between the Coulomb and LJ-PNE FE code.

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

Gerrit received a related patchset '1' for Issue #2640.
Uploader: Berk Hess ()
Change-Id: gromacs~release-2018~I193d55cf76d842f5b04d3a220411282c06b08a90
Gerrit URL: https://gerrit.gromacs.org/8333

#4 Updated by Berk Hess over 1 year ago

  • Status changed from Accepted to Fix uploaded
  • Assignee set to Berk Hess

The Coulomb forces were, incorrectly, scaled with lambda.
This bug (only) occurs when no charges are actually perturbed. Or, analogously, for LJ-PME when no atom types are actually perturbed.

#5 Updated by Berk Hess over 1 year ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Berk Hess about 1 year ago

  • Status changed from Resolved to Closed

#7 Updated by Mark Abraham 11 months ago

  • Related to Bug #2849: Free energy discrepancies between GROMACS versions added

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