Thank you very much. On Mar 12, 2018 14:51, "Justin Lemkul" <jalem...@vt.edu> wrote:
> > > On 3/12/18 9:48 AM, Amin Rouy wrote: > >> Ahan, thanks Justin. Is it default in all versions of Gromacs? >> > > As far as I remember, yes, but don't take my word for it. Look at > mdout.mdp from grompp - it has the full list of every setting that's being > used in your simulation (and also the top of md.log, though some of those > are parsed in ways that make them harder to understand). > > -Justin > > On Mon, Mar 12, 2018 at 2:44 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> On 3/12/18 9:31 AM, Mark Abraham wrote: >>> >>> Hi, >>>> >>>> Very many things are often simplified when you make a tutorial. Those >>>> .mdp >>>> files are already complicated enough for a beginner. >>>> >>>> Indeed, and comm-mode = linear is the default behavior, so it works just >>> fine without bothering the user to think about such abstract concepts :) >>> >>> -Justin >>> >>> >>> 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? 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. >>>>> >>>>> >>>>> -- >>> ================================================== >>> >>> 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? 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