On Mon, Mar 10, 2014 at 11:57 AM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > > If I could, I would RMS fit to the first frame the
> > > anchor, but RMSd rotates the box so this will kill imaging. Ideally, I
> > > would figure out how much in X,Y, and Z the anchor has moved and then
> > > translate back or do an RMS fit without rotation (which I do not think
> is
> > > possible at present...
> >
> > There is indeed a "norotate" option to the rmsd command in recent
> versions
> > of cpptraj....
>
> D'oh. Maybe I should read our manual! Then, what I would do is pick a
> lipid residue of interest, rms fit to that with norotate to the first
> frame, and then autoimage. Dan/Jason, you can let us know if this will
> not work. --tec3
>
I thought a simple "center" command would work (since that should translate
that lipid in every frame back to the origin) followed by an "image origin
center" which would image around that point. I suggested only a single
atom on the tail-end of the lipid just to drop the origin as close to the
'center' of the bilayer as possible, but for a large box the COM of a lipid
and the center of the bilayer is probably close enough.
That said, I don't see why a rms fit with norotate would fail to work...
The autoimage command may still be the best approach since that should
handle translating a particular lipid (in this case the first lipid
molecule) to the center of the box in every frame and imaging the rest of
the bilayer around it.
The OP can experiment with the different approaches to see which one fits
best...
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 10 2014 - 10:00:03 PDT
