Bug #1445
g_sas computes incorrect values with -nopbc
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
History
#1 Updated by Gerrit Code Review Bot almost 5 years ago
Gerrit received a related patchset '1' for Issue #1445.
Uploader: Teemu Murtola (teemu.murtola@gmail.com)
Change-Id: I798fc8fe96608633f26d9a3500f83f39b44af008
Gerrit URL: https://gerrit.gromacs.org/3199
#2 Updated by Teemu Murtola almost 5 years ago
- Status changed from In Progress to Fix uploaded
#3 Updated by Teemu Murtola almost 5 years ago
- Status changed from Fix uploaded to Resolved
- % Done changed from 0 to 100
Applied in changeset a56228accb8dc04c7ef08fe6bfc7518da43c218d.
#4 Updated by João M. Damas almost 5 years ago
Teemu Murtola wrote:
Applied in changeset a56228accb8dc04c7ef08fe6bfc7518da43c218d.
Conclusion on this issue: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/087665.html
#5 Updated by Roland Schulz over 4 years ago
- Status changed from Resolved to Closed
Fix incorrect grid cell size in g_sas -nopbc
Fixes #1445
Change-Id: I798fc8fe96608633f26d9a3500f83f39b44af008