VMD-L Mailing List

From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Tue May 09 2006 - 08:21:44 CDT

Hi All:

According to John, if wrapAll is set, then all coordinates including
solute molecule's will be wrapped into the periodic cell when being
written to output files. From your experience, it looks like the
solute molecule's coordinates are not wrapped. I am puzzled :(

Is there anyone anyone who is more familiar with NAMD can explain this?

marc
On May 8, 2006, at 9:57 PM, 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
>