What I notice is that imaging by the offsets works for about half of all of
the contacts I wish to 'pick-up' from my simulation. I have tested several
combinations of chain/center/image selections, and cannot figure-out why
this may be the case (i.e. I do not see a pattern in the X,Y,Z or chain
selections in the cases that do not pick-out the desired chains). For
example, this case works,
center :1-132
image :67-132 xoffset 0 yoffset -1 zoffset 0
whereas this case does not work,
center :1-132
image :67-132 xoffset -1 yoffset -1 zoffset -1
I have made sure that my parameter/topology file contains the proper
periodic boundary dimensions. Are there any suggestions for what may be the
issue and for how to get around it?
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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 13 2010 - 12:30:03 PST
