On 3/7/18 6:24 AM, Faezeh Pousaneh wrote:
Dear Justin, I have 2 questions regarding your tutorial on Carbon Dioxide in this link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html 1- I see that in your simple simulation you use no boundary conditions, pbc=no, should it be always so for this model? 2- You use comm-mode = angular, is that necessary?
The simulation is a simple gas-phase system, which does not use PBC and hence requires angular COM motion removal.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.