Project

General

Profile

Bug #3051

Minimization hangs with constraints and soft-core potentials

Added by Kevin Boyd 4 months ago. Updated 4 months ago.

Status:
Rejected
Priority:
Normal
Assignee:
-
Category:
mdrun
Target version:
Affected version - extra info:
Confirmed on 2019.3 and current master
Affected version:
Difficulty:
uncategorized
Close

Description

Minimization stops at step 0 and does not exit in a coarse-grained system with constraints and soft-core potentials. Running -DFLEXIBLE to turn constraints to harmonic bonds works, but I don't think this combination should silently fail.

Can reproduce with-
gmx grompp -f minimization.mdp -p buckle.top -c buckle-membrane-water.pdb
gmx mdrun -v -nsteps 5

buckle.top (180 Bytes) buckle.top Kevin Boyd, 07/31/2019 11:26 PM
martini_v2.2.itp (49.7 KB) martini_v2.2.itp Kevin Boyd, 07/31/2019 11:26 PM
martini_v2.0201506_lipids.itp (592 KB) martini_v2.0201506_lipids.itp Kevin Boyd, 07/31/2019 11:26 PM
minimization.mdp (1.02 KB) minimization.mdp Kevin Boyd, 07/31/2019 11:26 PM
buckle-membrane-water.pdb (7.73 MB) buckle-membrane-water.pdb Kevin Boyd, 07/31/2019 11:26 PM

History

#1 Updated by Berk Hess 4 months ago

  • Status changed from New to Rejected

You are requested free-energy and (mis)using harmonic bond parameters as constraint parameters. Thus the B-state constraint length is set to the bond force constant. This gives long bond lengths and PBC unwrapping takes very long.

Also available in: Atom PDF