Hi, Very many things are often simplified when you make a tutorial. Those .mdp files are already complicated enough for a beginner.
Mark On Mon, Mar 12, 2018 at 2:26 PM Amin Rouy <aminrou1...@gmail.com> wrote: > 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? 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