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Bug #1164

rlistlong seems not to work correctly for grompp warning

Added by Mark Abraham almost 5 years ago. Updated almost 4 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
4.5.5, 4.6
Affected version:
Difficulty:
uncategorized
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Description

Francesco reported an error with rlistlong= 1.4 and rvdw = rlist = 1.2 in http://lists.gromacs.org/pipermail/gmx-users/2013-February/079049.html. It looks to me like this error message should notice that rlistlong > rlist by enough that the size of the reported charge group is not an issue.

rlistIssue.tgz (1.06 MB) rlistIssue.tgz Chris Neale, 02/26/2013 10:32 PM

Associated revisions

Revision 3767b639 (diff)
Added by Berk Hess almost 5 years ago

corrected grompp rvdw charge-group radii check

The grompp note for charge-group radii larger than the buffer size
for VdW interactions only checked for rlist, not rlistlong.
Fixes #1164

Change-Id: I85a615e6c004503440bcae52c220540a843107d0

Revision e596fdd9 (diff)
Added by Berk Hess over 4 years ago

corrected grompp rvdw charge-group radii check

The grompp note for charge-group radii larger than the buffer size
for VdW interactions only checked for rlist, not rlistlong.
Fixes #1164

Change-Id: I85a615e6c004503440bcae52c220540a843107d0

History

#2 Updated by Chris Neale almost 5 years ago

Here are the files to reproduce the grompp note in version 4.5.5.

NOTE 2 [file empty.mdp]:
The sum of the two largest charge group radii (0.000000) is larger than
rlist (1.000000) - rvdw (1.500000)

Where rlist - rvdw is actually a negative value.

Thank you.

#3 Updated by Berk Hess almost 5 years ago

  • Status changed from New to In Progress
  • Assignee changed from Mark Abraham to Berk Hess

I uploaded a fix to gerrit.

#4 Updated by Mark Abraham over 4 years ago

  • Status changed from In Progress to Resolved
  • Affected version set to 4.6.1

#5 Updated by Mark Abraham over 4 years ago

  • Status changed from Resolved to Feedback wanted

This is an exact reversion of commit 662a4eb3add3. Do we really know what we're doing?

#6 Updated by Mark Abraham over 4 years ago

  • Target version changed from 4.6.2 to 4.6.3

#7 Updated by Berk Hess over 4 years ago

  • Status changed from Feedback wanted to Resolved
  • % Done changed from 0 to 100

#8 Updated by Rossen Apostolov almost 4 years ago

  • Status changed from Resolved to Closed

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