VMD-L Mailing List

From: Mauricio C. Tripp (trippm_at_wabash.edu)
Date: Tue Jan 06 2004 - 13:32:31 CST

Cool! I wasn't aware of the 'periodic' tab, sorry.
Now, I'm reading a charmm dcd trajectory file for
an NPT simulation. I guess VMD doesn't read the
correct box size for each frame; when I click
on the +/- x-,y-,z-button the corresponding image cell
is displayed but almost on top of the central cell.
However, if I run the script set_unitcell.tcl it
places the image cell acording to the box
dimensions I use as parameters for the script.
My next problem is that since I'm looking at a
NPT simulation, the box dimension will change from
frame to frame. Is there a way to modify the script
so it would set the correct box dimensions to
each frame and just not the same parameters for
the whole trajectory?

>===== Original Message From axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de =====
>On Tue, 6 Jan 2004 11:25:51 -0500 "Mauricio C. Tripp" wrote:
>
>> Hi all,
>>
>> does anyone know an easy way to display the
>> periodic image cells once I load the central
>> box into VMD, not just wrap the atoms in it?
>> any script to do this for a trajectory?
>
>hi mauricio,
>
>you won't need this with a sufficiently current
>vmd version. there is a tab 'periodic' in the
>graphical representation menu. just click on
>+/- x-,y-,z-button and you'll get copies of your
>unit cell for the current representation.
>in case your coordinate file(s) do not provide
>sufficient information about the unit cell,
>or vmd does not (yet) read this information,
>you need to run a small script like the attached tcl subroutine
>to set the unit cell parameters for each frame of your
>trajectory.
>
>hope this helps,
> axel kohlmeyer.
>
>>
>>
>> thank you
>>
>> Mauricio C. Tripp
>>
>
>--
>
>=======================================================================
>Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
>Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
>Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
>D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de
>=======================================================================
>If you make something idiot-proof, the universe creates a better idiot.