Project

General

Profile

Bug #3067

constraints = all-angles does not convert angles to constraints

Added by Marvin Bernhardt 3 months ago. Updated 3 months ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

I try to simulate united-atom propane gas (no LJ) with fixed C-C-C angle. For this I simply try to set constraints = all-angles in the mdp file, as this should:

    Convert all bonds to constraints and all angles to bond-constraints.
(from http://manual.gromacs.org/2019.3/user-guide/mdp-options.html#bonds)

However It does not have an effect. This i conclude from measuring the RDF between the CH3 groups, and the above option does not change the width of the peak. Also i can see the peaks in the vibrational density of states.

In the md.log i find:

The number of constraints is 4000

but it should be 6000 because there are 2000 molecules.

grompp outputs

turning all bonds and angles into constraints...

but apparently it doesn't happen. My current guess is that this is a grompp bug.

grompp.mdp (504 Bytes) grompp.mdp Marvin Bernhardt, 08/26/2019 01:45 PM
topol.top (842 Bytes) topol.top Marvin Bernhardt, 08/26/2019 01:45 PM
conf.gro (404 KB) conf.gro Marvin Bernhardt, 08/26/2019 01:45 PM

Associated revisions

Revision 9fee6b57 (diff)
Added by Berk Hess 3 months ago

Fix grompp constraints=all-angles with constraints

When using the mdp option constraints=all-angles, angles involving
bonds supplied as constraints in the topology would be removed,
but not replaced by angle constraints.

Fixes #3067

Change-Id: I7db390785a23c67abb30ae98e12272f88f5d5af7

History

#1 Updated by Berk Hess 3 months ago

  • Status changed from New to Fix uploaded
  • Assignee set to Berk Hess
  • Target version set to 2019.4

The angle constraint is missing, because of a bug when your topology contains constraints instead of bond potentials.
I uploaded a fix for release-2019.

#2 Updated by Berk Hess 3 months ago

  • Status changed from Fix uploaded to Resolved

#3 Updated by Paul Bauer 3 months ago

  • Status changed from Resolved to Closed

Also available in: Atom PDF