Dear Justin, If we do not use comm-mode, which quantity might be changed after simulations?
Can we remove center of mass after the simulation done? On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy <aminrou1...@gmail.com> wrote: > thank you so much. > > On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 3/10/18 12:31 PM, Amin Rouy wrote: >> >>> Thank you Justin. >>> What if we do not know the phase of the final result? of if we are in 2 >>> phase region (gas-liquid) >>> >> >> If you're applying PBC you have to use linear as your comm-mode (grompp >> will fail otherwise, so that's a pretty good hint). >> >> -Justin >> >> >> On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> On 3/10/18 12:17 PM, Amin Rouy wrote: >>>> >>>> Dear Gromacs people, >>>>> >>>>> I have a question please. >>>>> >>>>> In which condition we must use center of mass removal? Is that >>>>> optional or >>>>> necessary? >>>>> >>>>> Typically necessary. >>>> >>>> and how to know which mode (linear or angular) is better for our >>>> >>>>> simulations? >>>>> >>>>> Linear is only for condensed-phase systems, angular is only for vacuum >>>> simulations. >>>> >>>> -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. >>>> >>>> >> -- >> ================================================== >> >> 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.