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Bug #1590

COM pulling in geometry cylinder does not conserve energy

Added by Berk Hess about 5 years ago. Updated over 4 years ago.

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

The COM pull geometry cylinder uses weighting based on the radial distance with the cylinder reference group. This weighting leads to radial forces. These radial forces are currently ignored (because they are tedious to calculate and they produce inconvenient compression/extension forces). This means that force is not the gradient of the potential and energy is not conserved (although the errors are small for large cylinder radii).

Associated revisions

Revision dbe80640 (diff)
Added by Berk Hess over 4 years ago

COM pulling options per coord, improved cylinder

The COM pull type (potential/constraint), geometry, dimensions
and pull-start can now be set differently for each pull coordinate.
Also added a flat-bottom potential.

Cylinder geometry now uses a smooth radial weight function and
adds radial forces so it now conserves energy.
Fixes #1590.

There is now also an option for printing the COM of the second group,
as well as the reference value for all pull coordinates.
Writing the distance components to the pull coordinate output is now
optional (off by default).

gmx wham currently only supports input with the old restrictions
(and it checks for this). These restrctions should be removed.

Change-Id: I86e443b225accb85cc7fe0aa6c23d937f15b2efb

History

#1 Updated by Gerrit Code Review Bot over 4 years ago

Gerrit received a related patchset '29' for Issue #1590.
Uploader: Berk Hess ()
Change-Id: I86e443b225accb85cc7fe0aa6c23d937f15b2efb
Gerrit URL: https://gerrit.gromacs.org/3947

#2 Updated by Mark Abraham over 4 years ago

  • Status changed from In Progress to Closed

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