Archive from user: James Barnett In md.log when using the pull code, there is always a “pull-group 0” output with no atoms. grompp does not accept “pull-group0-name”, etc, so the count should start at 1. Additionally, pull-ngroups always is set to one number higher than the actual number of pull groups set. For example, setting “pull-ngroups” to 2 in the mdp file results in the md.log stating that “pull-ngroups” is 3; the processed mdp file has the correct number. Additionally later in the log it states (using to virtual sites in this one, so no masses): Will apply potential COM pulling with 1 pull coordinate and 3 groups Pull group 1: 1 atoms, mass 0.000 Pull group 2: 1 atoms, mass 0.000 *(from redmine: issue id 2143, created on 2017-03-20 by gmxdefault, closed on 2018-01-02)* * Changesets: * Revision fba92a59628c0fb04f7c2b6f110ab357fe6861ef by Erik Lindahl on 2018-01-02T11:12:37Z: ``` Don't write reference pull group 0 to log This is an internal group used for absolute references, which cannot be set by users, so printing it just leads to confusion. Fixes #2143. Change-Id: I89ee3a0e3a65855735b745f4ed7615ca47bfd36a ``` * Revision 3891bbbbc5f80e71b418ada70cc93c08911c301b by Berk Hess on 2018-04-03T07:21:27Z: ``` Do not calculate COM for pull group 0 Pull group 0 is an absolute reference with coordinates 0,0,0, so it is clearer to never compute its center of mass. Refs #2143 Change-Id: Ifa974ab84afe303594c3b65e9567e0568bb151a9 ```