Dear Justin One more question please, Do we need to have constraint in this model of CO2? Isn't it so that we have fixed the bond lengths and angles (180) in the topology by this method?
I run 2 simulations, one with constraints = all-angles and the other with constraints = all-bonds, I get different results from them. Why? Best regards On Wed, Mar 7, 2018 at 2:54 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > Thank you. > > > Best regards > > > On Wed, Mar 7, 2018 at 1:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> 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. >> > > -- 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.