But, why in some Gromacs tutorial there is no comm-mode used in .mdp file, for example in 'Lysozyme in water';
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html On Mon, Mar 12, 2018 at 1:50 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > If you get this wrong, the equipartition of energy is usually broken and > the simulation is probably unphysical. > > Mark > > On Mon, Mar 12, 2018, 13:47 Amin Rouy <aminrou1...@gmail.com> wrote: > > > 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. > > > -- > 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.