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Bug #1923

Number of degrees of freedo too small for 1D and 2D systems

Added by Berk Hess over 3 years ago. Updated over 3 years ago.

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

With center-of-mass-motion removal (on by default), grompp will subtract DOFs for dimensions that are completely frozen. This leads to a too small, and zero for 2 atoms in 1D, number of degrees of freedom. This in turn leads to incorrect temperature coupling with MD. SD and BD give correct sampling, but might report incorrect temperatures.

Associated revisions

Revision 5e7178f0 (diff)
Added by Berk Hess over 3 years ago

Correct nrdf for 1D/2D systems

With COMM removal, grompp would subtract degrees of freedom also for
VCM groups with fully frozen dimensions, i.e. 1D/2D systems.
Also fixed division by zero for groups with #DOF=0 with VV.

Fixes #1923.

Change-Id: I0ba2535df0495947d9bbb6ee1ef29f519635c221

History

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

Gerrit received a related patchset '1' for Issue #1923.
Uploader: Berk Hess ()
Change-Id: I0ba2535df0495947d9bbb6ee1ef29f519635c221
Gerrit URL: https://gerrit.gromacs.org/5726

#2 Updated by Berk Hess over 3 years ago

  • Status changed from In Progress to Fix uploaded

#3 Updated by Erik Lindahl over 3 years ago

  • Status changed from Fix uploaded to Resolved

#4 Updated by Erik Lindahl over 3 years ago

  • Status changed from Resolved to Closed

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