I was not thinking about this clearly yesterday evening. So long as I strip
everything that I do not want from my trajectory, there is no reason why
imaging by offsets should not work. I will give this a go... thanks again.
Sincerely,
Logan
On Sat, Dec 11, 2010 at 5:19 PM, Thomas Cheatham III <tec3.utah.edu> wrote:
>
> > I have investigated this issue with several test cases with both ptraj
> and
> > VMD (and checked the ptraj source code in action.c). Simply translating
> does
> > not take into account the gamma=120 angle of my unit cell, i.e.
> translation
> > does not reproduce the periodic images from my simulation. As a result, I
> am
> > not obtaining the correct interfaces in my filtered trajectory. Does
> anyone
> > know of a way to translate along unit cell dimensions that are not all
> > orthogonal to one another?
>
> As you observe, the translate command has no concept of the periodic unit
> cell... Moreover, unless the periodic box was fixed (constant volume) and
> the molecules fairly rigid you would have a difficult time predicting for
> each frame what distance should be translated to preserve the interface...
>
> I think what you want is not "translation" but imaging, and instead of
> imaging to the unit cell, imaging to nearby unit cells. This can be done
> using the xoffset/yoffset/zoffset values to the image command. I also see
> that I neglected to add this to the manual (d'oh!).
>
> If you want to image your molecule, say residues 1-100 to the unit cell in
> the +x direction,
>
> image :1-100 xoffset 1.0
>
> To, for example, build up a whole series of unit cells around my original
> cell I run ptraj multiple times with all combos +/- 1.0, 0.0 to get this.
> See a csh script below.
>
> --tec3
>
>
> build_crystal.csh:
>
> #!/bin/csh -f
>
> set rst = $1
>
> foreach x (0 1 2)
> foreach y ( 0 1 2)
> foreach z ( 0 1 2 )
>
> ptraj prmtop <<EOF
>
> trajin $rst
> trajout img_$x$y$z.pdb pdb
> strip :WAT
> center :1-24
> image xoffset $x yoffset $y zoffset $z
>
> EOF
>
> mv img_$x$y$z.pdb.1 img_$x$y$z.pdb
> end
> end
> end
>
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Received on Sun Dec 12 2010 - 06:30:06 PST
