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Bug #1445

g_sas computes incorrect values with -nopbc

Added by Teemu Murtola about 3 years ago. Updated about 3 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
analysis tools
Target version:
Affected version - extra info:
4.0.?-4.6.5
Affected version:
Difficulty:
uncategorized
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Description

g_sas computes incorrect surface areas if -nopbc is specified. The problem has been introduced some time in the 4.0.x series, probably between 4.0 and 4.0.3 (e2045413, merged to development version in 1437fac0). The cell size of the grid used to search for neighboring atoms is determined as the radius of the first atom instead of double the maximum radius as it should.

Additionally, the 4.0.x series g_sas always triggers the -nopbc option (ed04b50), irrespective of what is provided on the command line (and thus always produces the incorrect result).

This explains at least some of the results reported on gmx-users: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-February/087460.html

Associated revisions

Revision a56228ac (diff)
Added by Teemu Murtola about 3 years ago

Fix incorrect grid cell size in g_sas -nopbc

Fixes #1445

Change-Id: I798fc8fe96608633f26d9a3500f83f39b44af008

History

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

Gerrit received a related patchset '1' for Issue #1445.
Uploader: Teemu Murtola ()
Change-Id: I798fc8fe96608633f26d9a3500f83f39b44af008
Gerrit URL: https://gerrit.gromacs.org/3199

#2 Updated by Teemu Murtola about 3 years ago

  • Status changed from In Progress to Fix uploaded

#3 Updated by Teemu Murtola about 3 years ago

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

#5 Updated by Roland Schulz about 3 years ago

  • Status changed from Resolved to Closed

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