VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 07 2006 - 10:05:19 CST

Michel,
  VMD should indeed preserve PBC unit cell information when writing a
new trajectory based on an old one that contained unit cell info.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 07, 2006 at 05:01:14PM +0100, L. Michel Espinoza-Fonseca wrote:
> thanks!
>
> It makes the things clearer... and about the dcd, I created it WITH
> vmd from a bigger trajectory, and I'm not sure if the cell information
> is stored in it... Just wondering :)
>
> Cheers,
> Michel
>
> 2006/3/7, Axel Kohlmeyer <akohlmey_at_vitae.cmm.upenn.edu>:
> > On Tue, 7 Mar 2006, L. Michel Espinoza-Fonseca wrote:
> >
> > michel,
> >
> > please RTFM,
> >
> > you have to put whatever you want to _keep_ centered
> > into the selection text, i.e. protein or "not water",
> > because the moving is done w.r.t. to the center of
> > mass of this selection. if you use water, it will
> > not do a useful thing.
> >
> > also if you have a dcd file _with_ the unitcell information,
> > than you don't need to use the set_unitcell script.
> >
> > regards,
> > axel.
> >
> > ME> Hi Axel,
> > ME>
> > ME> I tried to do what you suggested me, but it didn't work. Maybe I did
> > ME> it wrong. First, I used the script called "moveframes.tcl" as:
> > ME>
> > ME> moveframes top water
> > ME>
> > ME> then I continued to the next steps to set PBC (my file is in DCD
> > ME> format). Then I tried to perform the analysis I wanted to, but I got
> > ME> the same results.
> > ME>
> > ME> Do you have any suggestions?
> > ME>
> > ME> Thanks!
> > ME>
> > ME> Michel
> > ME>
> > ME> 2006/3/6, Axel Kohlmeyer <akohlmey_at_vitae.cmm.upenn.edu>:
> > ME> > On Mon, 6 Mar 2006, L. Michel Espinoza-Fonseca wrote:
> > ME> >
> > ME> > dear michel,
> > ME> >
> > ME> > if you have enough water around your peptide, the following may work:
> > ME> >
> > ME> > load the trajectory, then use a hacked version of the fitframes
> > ME> > script, that does only move the selection, and apply pbc.
> > ME> >
> > ME> > depending on your trajectory format (some do store the box information,
> > ME> > some not), you have to set the box dimensions as well (see set_unitcell)
> > ME> > and then apply pbc based on the thusly stored info (i have used a hacked
> > ME> > version of pbcwrap for that, attached). so that in the end you you
> > ME> > something like:
> > ME> >
> > ME> > source set_unitcell.tcl
> > ME> > source pbcwrap.tcl
> > ME> > mol new TRA1_axel.xyz waitfor all
> > ME> > set_unitcell 11.0 11.0 11.0
> > ME> > pbcwrap
> > ME> > animate goto 0
> > ME> >
> > ME> > and then do your analysis.
> > ME> >
> > ME> > good luck,
> > ME> > axel.
> > ME> >
> > ME> >
> > ME> > MEF> Dear all,
> > ME> > MEF>
> > ME> > MEF> I've been trying to analyze the contacts between water and a given
> > ME> > MEF> peptide from my trajectories. I used a nice script provided by one of
> > ME> > MEF> the VMD users. Everything went well, except from the fact that VMD is
> > ME> > MEF> not able to count the water molecules around my peptide from the image
> > ME> > MEF> of my periodic box. I've read some issues related to the pbc and VMD
> > ME> > MEF> (computation of hbonds, for instance), and according to what I read,
> > ME> > MEF> there is not such handling of pbc in VMD. Do you have any suggestions?
> > ME> > MEF> I tried to use some artifacts such as drawing images of the water box,
> > ME> > MEF> but it didn't work.
> > ME> > MEF>
> > ME> > MEF> Thanks!
> > ME> > MEF>
> > ME> > MEF> Michel
> > ME> > MEF>
> > ME> >
> > ME> > --
> > ME> > =======================================================================
> > ME> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > ME> > Center for Molecular Modeling -- University of Pennsylvania
> > ME> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > ME> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > ME> > =======================================================================
> > ME> > If you make something idiot-proof, the universe creates a better idiot.
> > ME> >
> > ME> >
> > ME> >
> > ME>
> >
> > --
> > =======================================================================
> > 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.
> >
> > 

-- 
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