Hi users/developers, I identified 2 issues in the center_coords function of g_density that make the flag -center incorrectly center the system. These are in addition to the issues previously raised by Chris Neale (reported as issue 1168 on redmine: http://redmine.gromacs.org/issues/1168). I have added these two issues to the same redmine bug report as they are related to the same analysis tool/similar issues; following from Chris' previous advice, I also suggest that users not use the -center flag and instead center their trajectories prior to running g_density using trjconv. The issues described below are present in g_density for GMX 4.6 and presumably for earlier/later versions as well; I apologize if these have been updated in 4.6.1 or 4.6.2.
The function center_coords is intended to shift the COM of the system to bX/2, bY/2, 0 as described in the help documentation for bCenter. This is accomplished by calculating a shift vector on line 153 (line numbers may be off, sorry): rvec_sub(box_center, com, shift); and then subtracting the shift from all coordinates in a loop on line 162: for (i = 0; (i < atoms->nr); i++) rvec_dec(x0[i], shift); This is incorrect; the shift vector should be added to all coordinates, not subtracted, for the COM to be centered since rvec_sub sets shift to box_center - com. This can be fixed by changing rvec_dec to rvec_inc, which I have verified returns the correctly centered coordinates. The other issue is that the COM is computed by weighting by the mass of each atom obtained from the topology, as shown in the command: mm = atoms->atom[i].m; This is fine if the -dens flag is set to mass or electron; but for number or charge the atom[i].m variable in the topology is reset in the function g_density to either 1 (for -dens number) or the atom's charge (for -dens charge). The system is thus centered not by the center of mass, but rather by the geometric center/center of charge respectively. This could be fine but may not be obvious to the user. Again I added a report of both issues to the redmine report and wanted to inform users of their existence in case this affects the use of the g_density tool. Best, Reid -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
