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

From: Joseph Baker <bakerj.tcnj.edu>
Date: Thu, 26 Feb 2015 18:13:44 -0500

Thanks all. Got sidetracked for a couple of days, but I've had a chance to
test this out now. What I've done is to find a water molecule in my system
that is about where I want to pull towards and then use a combination of
jar=1 for the pulling and ntr=1 to define restraints on that water to pin
it in place relative to the protein. I then used parmed to change the LJ
type (using the addLJType command) of that particular water molecule's
oxygen and hydrogens to new types with zero epsilon, and used the change
command in parmed to zero out the charges on those atoms. pmemd.cuda seems
to be able to run with this new output parm7 file and I am seeing my
protein be steered towards that dummy water molecule. Does this procedure
make sense?

--
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 Tue, Feb 24, 2015 at 7:40 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Mon, 2015-02-23 at 18:20 -0500, Joseph Baker wrote:
> > Okay. My applications are basically 1. pull on the COM a few monomers in
> a
> > filament while restraining monomers at the other end, along the filament
> > axis direction and 2. pull a protein that has a domain embedded in a
> > membrane out of the membrane. So it seems to me in both of those cases I
> > will probably want to keep the dummy atom as a fixed point using the
> ibelly
> > restraints, unless I am thinking about this incorrectly. However, it
> looks
> > like belly style restraints are also not currently supported in
> pmemd.cuda?
>
> Correct.  ibelly is not supported in pmemd.cuda (although the
> functionality to implement it *is* present).  An alternative to ibelly
> is positional restraints, which *is* implemented on the GPU.
>
> I agree with Adrian in that ibelly is not really an "ideal" solution
> here.  What happens when your protein naturally tumbles and that dummy
> particle is now positioned differently relative to the protein?  What
> you can do is tether that dummy atom to some atoms on the protein to fix
> the pull direction with respect to a constant frame of reference defined
> by the protein (not the arbitrary Cartesian space).
>
> Ideally you would then use constraints to *fix* that particle in space
> without having the steering force exert forces on other particles. To
> get pmemd.cuda to do this, you would need to convince it that your dummy
> particle is actually a hydrogen atom and turn on SHAKE. However, with
> the exception of water molecules, I don't think the CUDA code supports a
> single hydrogen having multiple distance constraints through SHAKE, so
> you may have to play around with a couple options to get it working.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Thu Feb 26 2015 - 15:30:02 PST