VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 09 2006 - 09:21:31 CDT

Guo,
  Your solute should also wrap, but only when it moves far enough, as
I believe NAMD only wraps whole segments at a time...

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 09, 2006 at 09:57:20AM +0800, Guo Zhi wrote:
> i set "wrapAll" option on in my MD. From VMD i saw that only the solute
> molecule is not wrapped, and the water molecules are always wrapped. So
> that I guess "atomselect top "water and name "O."" " maybe more reasonable?
> Thanks for your advices!
>
>
> 2006/5/9, John Stone <johns_at_ks.uiuc.edu>:
> >
> >
> >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.
> >> >>
> >> >>
> >> >
> >>
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> >WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078