VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_vitae.cmm.upenn.edu)
Date: Tue Mar 07 2006 - 09:55:27 CST

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.