Project

General

Profile

Bug #1343

vsiten particles are not integrated

Added by David van der Spoel almost 6 years ago. Updated almost 6 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
mdrun
Target version:
Affected version - extra info:
master branch
Affected version:
Difficulty:
uncategorized
Close

Description

Sometime in 2013 during the master branch development a bug was introduced that makes that the coordinates of vsiten particles are not integrated, that is they remain at the same position. In the attached example one has to change the particle type of the MW particle in amber99sb-ild.ff/ffnonbonded.itp to V (or D) to make it work, then

grompp -maxwarn 20
mdrun

gmx gmxdump -f traj.xtc | grep ' 1100\]'
x[ 1100]={ 5.35100e+00, 6.43100e+00, 5.72700e+00}
x[ 1100]={ 5.35100e+00, 6.43100e+00, 5.72700e+00}
x[ 1100]={ 5.35100e+00, 6.43100e+00, 5.72700e+00}
x[ 1100]={ 5.35100e+00, 6.43100e+00, 5.72700e+00}
x[ 1100]={ 5.35100e+00, 6.43100e+00, 5.72700e+00}

As you see the coordinates of this vsiten particle is exactly constant!
It works fine in 4.6 and earlier, as well as in older master branches. I tried git bisect but could not find the right position :(.

vsitebug.zip (68.6 KB) vsitebug.zip gro, mdp, top David van der Spoel, 09/27/2013 10:23 PM

Associated revisions

Revision cd41feab (diff)
Added by David van der Spoel almost 6 years ago

Fixes bug in processing virtual_sitesn in grompp.

Fixes #1343

Change-Id: Ia1d39199a12292ef86d086a6c1bb5f1a0bdb5d35

History

#1 Updated by David van der Spoel almost 6 years ago

Didn't mean to assign it to Berk just added him as a watcher. Will try more tomorrow :(.

#2 Updated by David van der Spoel almost 6 years ago

  • Status changed from New to Fix uploaded

#3 Updated by David van der Spoel almost 6 years ago

  • Status changed from Fix uploaded to Resolved
  • % Done changed from 0 to 100

#4 Updated by David van der Spoel almost 6 years ago

  • Status changed from Resolved to Closed

Also available in: Atom PDF