Feature #2339

sum of two largest charge group is enormous and bigger than rlist

Added by Mark Abraham over 2 years ago. Updated over 2 years ago.

preprocessing (pdb2gmx,grompp)
Target version:


grompp warns if a charge group is larger than rlist, but if it's crazy large then that might because of a PBC split, particularly if the group has few particles. If so, then a better warning would suggest that the solution is to make molecules whole. In fact, grompp could probably just do the latter routinely after building the topology, which might help for other things.

But if the warning can only happen with the group scheme, then let's not bother.

Associated revisions

Revision 930725b2 (diff)
Added by Paul Bauer over 2 years ago

Remove PBC before generating TPR with group scheme

Ensure that all molecules have been made whole before generating the
run input file when using the group scheme, to avoid error
messages for large charge groups when molecules are broken
over PBC boundaries.

Fixes #2339

Change-Id: Iecba013826cbe46e7f70bd674935f9946806ee2e


#1 Updated by Berk Hess over 2 years ago

  • Status changed from New to Closed

There are no charge groups with the Verlet scheme or you can view it a single atom charge groups, so this can't happen there.
So will not fix.

#2 Updated by Gerrit Code Review Bot over 2 years ago

Gerrit received a related DRAFT patchset '1' for Issue #2339.
Uploader: Paul Bauer ()
Change-Id: gromacs~release-2018~Iecba013826cbe46e7f70bd674935f9946806ee2e
Gerrit URL:

#3 Updated by Mark Abraham over 2 years ago

  • Status changed from Closed to Fix uploaded
  • Target version set to 2018-beta3

#4 Updated by Paul Bauer over 2 years ago

  • Status changed from Fix uploaded to Resolved

#5 Updated by Paul Bauer over 2 years ago

  • Status changed from Resolved to Closed

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