VMD-L Mailing List

From: Guo Zhi (gzgzgz_at_gmail.com)
Date: Tue May 09 2006 - 22:28:42 CDT

John:
    Yeah, you may be right, my protein has only 1/5 part of it move out of
the periodic box. But for small ligands, it seems that 1/2 part protrusion
shall result in an update.

2006/5/9, John Stone <johns_at_ks.uiuc.edu>:
>
>
> 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
>