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
>
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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/
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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 - 14:30:03 PST
