VMD-L Mailing List

From: dimka (newyorkdimka_at_gmail.com)
Date: Mon May 08 2006 - 12:08:53 CDT

if you used "wrapWater on" option in your simulations, i suppose you
can look at minmax of just water oxygens. This will probably give you
more-or-less accurate box size.

On 5/8/06, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
> On Mon, 8 May 2006, Guo Zhi wrote:
>
> GZ> Well, my system is NPT. I want to use "measure minmax [atomselect top
> water]" to calculate the unit cell info in each frame, is this recovery
> method correct?
>
> no, your cell will always be too large since molecules will always
> be wrapped as a whole.
>
>
> ---------- Forwarded message ----------
> From: Guo Zhi <gzgzgz_at_gmail.com>
> Date: 2006-5-7 ÏÂÎç11:32
> Subject: vmd-l: How to pick up the lost periodic information?
> To: vmd-l_at_ks.uiuc.edu
>
> Hi, VMD users:
> I forgot to include DCDunitCell option in my simulation. So that it
> seems that the dcd trajectory file does not include any periodic
> information( when i ticked any of the checkbox of +X, -X, +Y, -Y... none of
> them works ), but i really want to see the movie with smooth boundary
> connected, is it still possible? How to do it?
> What's more, how to select neighboring atoms that stride two periodic
> boxes?
>
> no, that is currently not possible. you have to duplicate the
> atom coordinates accordingly and the analyse.
>
> regards,
> axel.
>
> --
> ===============================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> ===============================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
>