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Bug #2286

Coulomb energies and forces incorrect with coulomb-type = pme-user

Added by Yu Du about 2 years ago. Updated almost 2 years ago.

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

Under group cutoff-scheme, simulation temperature only accords with the ref_t in nh-chain-length=1 in nose-hoover thermostat.

Using nh-chain-length!=1 of nose-hoover or v-rescale thermostat, I can't get the simulation temperature according with ref_t and the simulation temperature is higher than ref_t.

My system uses the tutorial materials from Lysozyme in Water

Topol file, mdp file and system after EM are attached.
The amber99sb-ildn of nbfunc=1 and comb-rule=1 version is here

The command I used:
gmx_mpi grompp -f nvt_group.mdp -c em.gro -p topol.top -o nvt_99sbildn_functype11_user.tpr

mpirun -np 20 gmx_mpi mdrun -quiet -ntomp 1 -nb cpu -notunepme -deffnm nvt_99sbildn_functype11_user

Thanks!

Yu

nh_group_problem.rar (478 KB) nh_group_problem.rar Yu Du, 11/02/2017 04:09 AM

Associated revisions

Revision 368b4463 (diff)
Added by Berk Hess about 2 years ago

Add missing Ewald correction for pme-user

With coulomb-type = pme-user, the Ewald mesh energy was not subtracted
leading to (very) incorrect Coulomb energies and forces.

Fixes #2286

Change-Id: Idfef9896d484e254264150e718c5516a832a2ad4

History

#1 Updated by Gerrit Code Review Bot about 2 years ago

Gerrit received a related patchset '1' for Issue #2286.
Uploader: Berk Hess ()
Change-Id: gromacs~release-2016~Idfef9896d484e254264150e718c5516a832a2ad4
Gerrit URL: https://gerrit.gromacs.org/7139

#2 Updated by Berk Hess about 2 years ago

  • Subject changed from Group cutoff-scheme and simulation temperature to Coulomb energies and forces incorrect with coulomb-type = pme-user
  • Status changed from New to Fix uploaded
  • Priority changed from Normal to High
  • Target version set to 2016.5
  • Affected version changed from 2016.3 to 2016

This is not a temperature coupling issue, but a bug in the pme-user interaction implementation. I uploaded a fix for this.
Release 5.1 and before do not seem to be affected by this.

PS You should never change the combination rule of a force field. The warning in grompp is given for the case a user makes his/her own force field.

#3 Updated by Berk Hess about 2 years ago

  • Status changed from Fix uploaded to Resolved

#5 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Resolved to Closed

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