Thanks, Justin. I am trying to understand what is meant by 'com' option. Following two sentences in manual seem conflicting with each other:
"*Scale* the center of mass of the reference coordinates with the scaling matrix of the pressure coupling. The *vectors of each reference coordinate*to the center of mass are *not scaled*." Doesn't scaling center of mass of reference coordinates change something else ? reference coordinates? Thanks Chetan On Mon, Mar 24, 2014 at 8:22 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/24/14, 9:05 PM, Chetan Mahajan wrote: > >> Hi Justin, >> >> My system is TiO2 crystal (2160 atoms position restrained) solvated by >> 3656 >> water molecules, 1 formate anion and 1 sodium ion. Is it true that when >> 'all' option is used, positions of the atoms (meant to be restrained) >> always change? >> >> > Consider what position restraints are doing. They never guarantee that > atoms won't move; they just apply a biasing potential to disfavor movement. > So yes, your atoms will probably move. The smaller the system, the larger > the effect will likely be. Consider also what reference coordinates are > doing. They define how strong the potential is (distance between current > coordinates and reference). If you're scaling all atoms individually > according to the pressure coupling, the reference moves and therefore the > atoms can also move. For larger systems like proteins, "refcoord_scaling = > com" is normal and stable, and "refcoord_scaling = all" is disfavored. > Honestly, I don't know what to expect for a very small system like yours, > but it is likely to be affected to a greater extent. > > If the "all" option gives you a stable simulation that allow for proper > equilibration, then I doubt there is any real problem. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.