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-- Joseph Baker, PhD Assistant Professor Department of Chemistry C101 Science Complex The College of New Jersey Ewing, NJ 08628 Phone: (609) 771-3173 Web: http://bakerj.pages.tcnj.edu/ <https://sites.google.com/site/bakercompchemlab/> On Mon, Feb 23, 2015 at 5:35 PM, Adrian Roitberg <roitberg.ufl.edu> wrote: > almost... > > If you want to pull/push just in a direction, then yes, that works. > However, keep in mind that both your molecule AND the dummy atom will > move towards or away from each other, not just the molecule. > > You could keep the dummy atom fixed in space through belly, etc, but be > very careful with that, belly has some nasty surprises around... > adrian > > On 2/23/15 5:32 PM, Joseph Baker wrote: > > Thanks, Adrian. So basically just define some new atom type that has zero > > LJ and Coulomb interactions (so only a mass), put that at the location I > > want to pull towards, and use the jar=1 option as usual? If that's it, it > > sounds straightforward enough. > > > > Joe > > > > > > -- > > Joseph Baker, PhD > > Assistant Professor > > Department of Chemistry > > C101 Science Complex > > The College of New Jersey > > Ewing, NJ 08628 > > Phone: (609) 771-3173 > > Web: http://bakerj.pages.tcnj.edu/ > > <https://sites.google.com/site/bakercompchemlab/> > > > > On Mon, Feb 23, 2015 at 5:13 PM, Adrian Roitberg <roitberg.ufl.edu> > wrote: > > > >> Hi > >> > >> Your reading of what is available is correct. > >> > >> Unfortunately, there is no way now to pull in a particular direction. > >> What we have done in the past is to add an atom in space and pull/push > >> using the distance between your desired group of atoms and that > >> atom/molecule. If you are clever enough, you can set that point is space > >> to be 'dummy', meaning that it does not interact with the molecule > >> except for the spring you are adding with jar. > >> > >> adrian > >> > >> On 2/23/15 5:07 PM, Joseph Baker wrote: > >>> Hi all, > >>> > >>> So I've gathered that ncsu_smd support is not available for steered MD > in > >>> pmemd.cuda, but jar=1 is. I've also seen that I can define groups and > not > >>> just single atoms for the steered MD pulling (so that the distance that > >> I'm > >>> changing is between the center of mass of two selections for example). > >>> However, is there a way to specify the direction of pulling (along some > >>> vector for example) when using jar=1? Thanks for any input. > >>> > >>> Kind regards, > >>> Joe > >>> > >>> -- > >>> Joseph Baker, PhD > >>> Assistant Professor > >>> Department of Chemistry > >>> C101 Science Complex > >>> The College of New Jersey > >>> Ewing, NJ 08628 > >>> Phone: (609) 771-3173 > >>> Web: http://bakerj.pages.tcnj.edu/ > >>> <https://sites.google.com/site/bakercompchemlab/> > >>> _______________________________________________ > >>> AMBER mailing list > >>> AMBER.ambermd.org > >>> http://lists.ambermd.org/mailman/listinfo/amber > >> -- > >> Dr. Adrian E. Roitberg > >> Professor. > >> Department of Chemistry > >> University of Florida > >> roitberg.ufl.edu > >> 352-392-6972 > >> > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > >> > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > -- > Dr. Adrian E. Roitberg > Professor. > Department of Chemistry > University of Florida > roitberg.ufl.edu > 352-392-6972 > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Feb 23 2015 - 15:30:02 PST