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 Tue Feb 24 2015 - 05:00:03 PST
