On Thu, Jul 11, 2013 at 1:17 PM, Steven Neumann <s.neuman...@gmail.com>wrote:
> Thank you. Another question: Does RDF depends on the mass of the atom? On > the one hand it gives different value of the force in equation of motion > but on the other hand velocities are rescaled with a thermostat. > > It does not. Provided that ergodicity applies to your calculation/system. No different value of the force, just of the acceleration. Dr. Vitaly V. Chaban > Steven > > > On Thu, Jul 11, 2013 at 12:57 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 7/11/13 7:54 AM, Steven Neumann wrote: > > > >> Dear Users, > >> > >> Can you please write me where gromacs does read the mass of each atom: > Is > >> that the [atoms] under [moleculetype] or from [atomtypes] ? I wish to > >> assign different mass for two different beads of the same type in my > >> topology. > >> > >> > > It is taken from [atoms]. The entries for mass in [atomtypes] are only > > used if the mass field is blank in the [atoms] directive, IIRC. Easy to > > check, of course, with gmxdump :) > > > > -Justin > > > > -- > > ==============================**==================== > > > > Justin A. Lemkul, Ph.D. > > Postdoctoral Associate > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 601 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> > | (410) > > 706-7441 > > > > ==============================**==================== > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > * Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
