VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Feb 15 2008 - 12:22:40 CST

On Fri, 15 Feb 2008, Thomas C. Bishop wrote:

TB>
TB> but why do I have to
TB> pbc box -shiftcenter { 4 4 4 }
TB>
TB> to get the box centered on the image of the system?
TB> (shouldn't the default centering on the unit cell center the box on the
TB> system)

at this point you have no information of the position of the
origin of your box and different MD codes have different
conventions for that. in fact, even the orientation of the
box is no longer known (only its shape), which creates problems
with PBC for systems in non-orthogonal cells.

TB> any reason why they should or should not all be same value?
TB> my system dimensions are
TB> {128.945908 95.184196 127.153168 90.000000 90.000000 90.000000}
TB>
TB> so I might expect 4 3 4 would work a bit better...and it does.

you'll have to pick those empirically. alternately you can
provide a selection to calculate the center of your system.
see the plugin documentation.

TB> I presume this has something to do w/ how I initially set up the
TB> simulation and how the PBC box size evolved during min/eq.
TB> but is there any way to determine the shift value from NAMD output
TB> files?

no. it is gone.

cheers,
   axel.

TB>
TB> thanks
TB>
TB> Tom
TB>
TB>
TB> On Thu, 2008-02-14 at 23:05 +0100, Olaf Lenz wrote:
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TB> >
TB> > Hi!
TB> >
TB> > Thomas C. Bishop wrote:
TB> > | 1) do the periodic images displayed with (graphics reps -> periodic ->
TB> > | +x ; -x etc....) get the PBD dimensions updated every step when
TB> > | displaying an animation of the trajectory?
TB> >
TB> > When you have loaded the periodic information, then yes. Not all formats
TB> > do actually save this information, but those that do work fine.
TB> >
TB> > | Since there is an exwithin command... how about a pbcwithin command?
TB> >
TB> > That would be a good thing. As far as I understood, the whole periodicty
TB> > issue is currently redesigned, so I think afterwards we will have
TB> > something comparable.
TB> >
TB> > | 3) is there a way to easily display the periodic box size
TB> > | e.g. a "show pbcbox" or "get pbc dimensions" command or some other way
TB> > | to obtain values for the PBC dimensions within VMD if it has read them
TB> > | from the DCD
TB> >
TB> > In fact, there is the "pbctools" plugin that can do all this and more:
TB> >
TB> > http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
TB> >
TB> >
TB> > Best regards
TB> >
TB> > Olaf
TB> >
TB> >
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TB> 

-- 
=======================================================================
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.