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?
Thanks Chetan On Mon, Mar 24, 2014 at 7:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/24/14, 8:29 PM, Chetan Mahajan wrote: > >> Thanks, Mark. So is 'all' option okay when positions of each of the atoms >> of TiO2 crystal (2160 atoms total) are restrained in space? Apparently, it >> does not seem correct, since positions of the atoms of TiO2 crystal change >> when 'all' option is applied. However, it does not give error as 'com' >> option does. >> >> > Is your system just a TiO2 crystal? Is there any solvent? If it's just a > crystal, I see no point in restraining anything. It is very unusual that > the "all" option of refcoord-scaling is more stable than "com" - normally > the opposite is true. But that also explains why the coordinates are > changing - the reference position of each individual atom is scaled > according to the pressure coupling matrix, so the atoms are restrained to a > dynamic reference, so it seems that it's not really accomplishing anything. > > -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.