VMD-L Mailing List

From: Guo Zhi (gzgzgz_at_gmail.com)
Date: Mon May 08 2006 - 20:57:20 CDT

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
>