Dear GROMACS users: The GROMACS manual says that the off-diagonal elements (of deform option) can be used to shear a solid or a liquid. Then, how should I set the "comm-mode" option (concern for removing center of mass translation) to get shear flow with this deform option? I'd tried "comm-mode=None" (no restriction of the center of mass motion) but it looks no difference with "comm-mode=Linear" concern on shear flow. Also, I'm wondering how the system temperature (from atomic velocities) was evaluated if I succeeded to get shear flow with this deform option (mean shear flow contribution will be extracted or not). Sorry if it was FAQ.
Regards, Makoto Yoneya, Dr. AIST, Tsukuba JAPAN -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
