[gmx-users] editconf -translate help

David van der Spoel spoel at xray.bmc.uu.se
Sun Jun 24 10:16:25 CEST 2007

Shayla Fitzsimmons wrote:
> I have a box which contains a slab of carbon (solid) that is centered within the
> box.  However, I want the slab to be at the very right side of the box - I know
> I must use editconf -translate to do this, however I cannot seem to make it
> work.
> The slab is centered has the same height and width (y and z coordinates) of the
> box, however it is one third of the length (the x coordinate).  Graphically, at
> the moment, it looks like this:
>  _____________________
> |       xxxxxxx       |
> |       xxxxxxx       |
> |_______xxxxxxx_______|
> Where 'xxxxxx' is my slab (that is how the view comes up when I open the file in
> rasmol).
> The dimensions of the box (as listed in the .gro file) are 13.90030 4.02160
> 5.36640
> As I previously said, I want the slab to be on the right side of the box, not
> the center, however I have tried several different things and it does not seem
> to want to work for me (however, I am unsure if I am using the proper values
> for -translate).
> What X Y Z coordinates should I use for this to translate it?

the difference between new and old com. most likely 5 0 0 will do the trick.

> Thanks!
> S F
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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