Hi, Using center of mass motion removal in combination with an absolute reference in the system, such as position restraints, will always lead to artifacts, as physical motion is removed and not drift due to numerical rounding errors. For the most common case of equilibrating macromolecules using position restraints these artifacts are usually negligible.
So we should probably add a sentence to the note: Removing center of mass motion in the presence of positions restraints might cause artifacts. When position restraints are used to equilibrate a macromolecule these artifacts are usually negligible. I think we should add a comm-removal setting "auto" which should be the default, so grompp can automatically turn off comm-removal when using position restraints. I realize now that we should check if there are no other artifacts when doing equilibration with position restraints in an NPT ensemble without comm-removal. I expect NVT should be fine without comm-removal. Cheers, Berk ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Christos Deligkaris <deligka...@gmail.com> Sent: Thursday, January 16, 2020 5:03 PM To: gmx-us...@gromacs.org <gmx-us...@gromacs.org> Subject: Re: [gmx-users] com motion and position restraints may cause artifacts The ambiguity in the gromacs 2020 note made me concerned, as it was not clear to me whether my system (DNA+small molecule) fills in the category where artifacts are caused. The gromacs note could have been a bit more helpful by referencing specific publications so that we can educate ourselves..... Best wishes, Christos Deligkaris, PhD On Thu, Jan 16, 2020 at 5:21 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 1/16/20 5:17 AM, Alessandra Villa wrote: > > Hi, > > > > On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris <deligka...@gmail.com> > > wrote: > > > >> dear all, > >> > >> I installed gromacs 2020 and I now get the following message during > >> equilibration: > >> > >> NOTE 1 [file nvt.mdp]: > >> > >> Removing center of mass motion in the presence of position > >> restraints might cause artifacts > >> > >> I do not recall seeing this with gromacs 2018. In which cases are > >> artifacts created? Is it now recommended to not remove the center of > >> mass motion during equilibration? > >> > >> > > It is recommended not to have position restrain and remove of center of > > mass at the same moment. That is also the case of the equilibration phase. > > That may cause artifact depending on the system and the condition you are > > simulating. > > What is the nature of these artifacts and where is this documented? > Combining position restraints with COM motion removal is an extremely > common practice. Phrases like "might cause artifacts" are troubling > because that implies uncertainty. Are there cases when this combination > does not cause artifacts? > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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.
