VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Mar 07 2006 - 10:28:34 CST

ooopa, now it worked!
Thanks for your help... and yes! it'll be nice to have and option that
enables PBC in VMD in the near future :)
Michel

2006/3/7, John Stone <johns_at_ks.uiuc.edu>:
>
> 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.
> > >
> > >
>
> --
> 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
>