Tested normal mode analysis with different small molecules. TIP5P gives NaN everywhere in the mtx file. TIP4P gives strange numbers as well, while models with shells yield weird numbers. I guess that in all cases mdrun should only work on the real atoms and not on the vsites/shells. *(from redmine: issue id 879, created on 2012-02-03 by dspoel, closed on 2016-07-11)* * Changesets: * Revision c289d8f778bcbd25dbcfbcd66115055168381914 by Rossen Apostolov on 2014-05-22T07:21:32Z: ``` Normal modes don't work currently with virtual sites or shells. Refs #879. Change-Id: I1c45b5a4b4c97feff222dccbbbb884e0153ad0c5 ``` * Revision 16f3a87b5be0847a292ad5c4dcdf4a967cb06e79 by David van der Spoel on 2016-01-07T08:14:51Z: ``` Made normal modes work with shells and vsites Implement shells and vsites in normal mode analysis (do_nm routine) and analysis of eigenvalues and frequencies. The normal mode analysis is done on real atoms only and the shells are minimized at each step of the analysis. Fixes #879 Change-Id: Iac127f51ef4ebd246c9d2417e039778b5952122f ```