Re: [AMBER] Steered MD using the jar=1 option

From: Joseph Baker <bakerj.tcnj.edu>
Date: Mon, 23 Feb 2015 17:32:46 -0500

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
>
>
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Received on Mon Feb 23 2015 - 15:00:03 PST