VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 08 2006 - 15:40:30 CDT

Marc,
  Actually NAMD _does_ write wrapped coordinates, but only if you
set the config option "wrapall on" in your NAMD config file..

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 08, 2006 at 03:05:31PM -0400, Marc Q. Ma wrote:
> Hi guys,
>
> Does NAMD write coordinates that are wrapped? I thought NO. My
> recollection is that NAMD only uses wrapping as a technique to
> calculate forces, and the DCD file output uses coordinates without
> wrapping.
>
> Please correct me if I am wrong.
>
> Marc
> On May 8, 2006, at 1:08 PM, dimka wrote:
>
> >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.
> >>
> >>
> >
> 

-- 
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