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
>>
>>
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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 - 15:00:03 PST
