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Bug #1901

grompp sets dihedral potentials based on order, not best match

Added by Berk Hess almost 4 years ago. Updated almost 3 years ago.

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

In the force field file dihedral parameter entries like
X CT CT X
should be placed after ones with the same types that don't use wildcards. This requirement does not seem to be documented. If you place such wildcard lines first, grompp will silently choose the wildcard match and will ignore the better match. Since Amber force field (modification) files put the wildcard ones first, this leads to high risks of near-silent incorrect results when users manually convert Amber force fields.

Associated revisions

Revision 607f4613 (diff)
Added by Berk Hess over 3 years ago

Remove restriction on dihdraltypes order

Wildcards are allowed for dihedraltypes by grompp. But it was assumed,
with only code and no user documentation, that wildcard types come
after fully specified types. If this order was switched, grompp would
silently choose the wildcard matches. Now the match with the most real
atom type matches is chosen.
Added a paragraph to the bonded parameter section in the manual on
dihedral wildcard matching.

Fixes #1901.

Change-Id: I7e44ff19e4d069d1b186ea470438a47d48f1a72d

History

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

Gerrit received a related patchset '1' for Issue #1901.
Uploader: Berk Hess ()
Change-Id: I7e44ff19e4d069d1b186ea470438a47d48f1a72d
Gerrit URL: https://gerrit.gromacs.org/5638

#2 Updated by Berk Hess almost 4 years ago

  • Status changed from In Progress to Fix uploaded

Uploaded fix that takes the match with the least wildcards instead of the first match and added documentation.

#3 Updated by Berk Hess 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

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

We just rediscovered this bug in old gromacs, thanks for fixing :) This should probably be added to the release notes however. It has probably led to errors in GAFF and OPLS simulations of non-proteins.

#6 Updated by Mark Abraham almost 3 years ago

David van der Spoel wrote:

We just rediscovered this bug in old gromacs, thanks for fixing :) This should probably be added to the release notes however. It has probably led to errors in GAFF and OPLS simulations of non-proteins.

Noted, will look into it.

#7 Updated by Mark Abraham almost 3 years ago

David van der Spoel wrote:

We just rediscovered this bug in old gromacs, thanks for fixing :) This should probably be added to the release notes however. It has probably led to errors in GAFF and OPLS simulations of non-proteins.

This fix is noted at http://manual.gromacs.org/documentation/5.1.3/ReleaseNotes/release-notes.html#removed-restriction-on-dihdraltypes-order. I'm open to suggestions for how to make stuff easier to find (or improvements to what is usually just my wording).

I hope to propose moving the infrastructure and source code into our repo(s) at some point, so that people can suggest their own text, and/or review at the eleventh hour before releases.

But the general problem of "how do I find whether this bug I have found (now or some time ago) was already fixed somewhere?" seems hard to solve other than choosing the right words and brute-force-thanks-to-Google.

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