Re: [AMBER] Translate command with ptraj

From: Logan Ahlstrom <>
Date: Sat, 11 Dec 2010 20:06:51 -0700

Thank you for the quick response. I have seen the C-shell script before that
you provided, and it has been quite useful. Indeed, I can usually 'pick-up'
the periodic neighbors via the "imaging" command, but due to the complexity
of the packing in my simulation (this is a crystal simulation) I cannot
always get the desired chain simply by imaging. Because of the details we
wish to investigate with crystal simulations, this trajectory was actually
run in the NVT ensemble. The thought I have at the moment is writing-out the
relationship to convert each dimension of my trigonal unit cell (a,b,c) back
to the orthogonal x,y,z dimensions. This would allow me to come-up with
combinations of x,y,z that reflect my crystal unit cell and, hopefully, then
translation would work. Does this sound reasonable?

On Sat, Dec 11, 2010 at 5:19 PM, Thomas Cheatham III <> 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 $z
> mv img_$x$y$z.pdb.1 img_$x$y$z.pdb
> end
> end
> end
> _______________________________________________
> AMBER mailing list

Logan S. Ahlstrom
Ph.D. Candidate
Department of Chemistry and Biochemistry
University of Arizona
Miyashita Lab
AMBER mailing list
Received on Sat Dec 11 2010 - 19:30:02 PST
Custom Search