VMD-L Mailing List

From: Lin (lavizgal_at_yahoo.com.sg)
Date: Fri Mar 24 2006 - 05:29:55 CST

--- Lin <lavizgal_at_yahoo.com.sg> wrote:

> Thank you for your reply! Sorry, im a novice in this
> area.
>
> Now, my algo is sth like this:
>
> readheader info
> push in natoms value into system
> push delta value into timestamp
>
> for nsets {
> for natoms {
>
> read in an int
> read X coordinates
> read in 2 int
> read Y coordinates
> reain in 2 int
> read Z coordinates
> read in an int
> }
> push delta into timstamp each time one frame is read
> in(i.e. nsets time)
> }
>
>
> is this how delta is utilised? or i do not need the
> delta
> value to separate the atoms into each frame?
>
> regards,
> lavina
> --- John Stone <johns_at_ks.uiuc.edu> wrote:
>
> > Hi,
> > nsets is the number of trajectory frames in the
> file,
> > natoms is the number of atoms, and delta is the
> > simulated
> > time between trajectory frames. Does that answer
> your
> > question?
> > You don't need delta in order to parse the file,
> delta
> > is just another
> > attribute that relates the stored coordinate sets
> with
> > the original
> > MD simulation parameters.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Mar 23, 2006 at 10:24:54AM +0800, Lin wrote:
> > > Hi, thank you. I have referenced to yje VMD DCD
> > plugin
> > > code. However, as my system works slightly
> > differently, i
> > > can only use the general idea of the code. Hence, I
> > am
> > > now having problem recognizing the atoms for each
> > frame.
> > > Is nsets the parameter to differentiate atoms from
> > each
> > > frame? or isst delta? what is the purpose of delta
> in
> > the
> > > reading of atoms?
> > >
> > > thanks!
> > >
> > > regards,
> > > lin
> > > --- John Stone <johns_at_ks.uiuc.edu> wrote:
> > >
> > > >
> > > > Hi,
> > > > The VMD DCD plugin (as well as the others) is
> > made
> > > > available
> > > > with the UIUC Open Source license, so you can
> just
> > use
> > > > our DCD
> > > > reader code if you like. Even if you prefer to
> > write
> > > > your own,
> > > > you might save yourself a lot of time and energy
> by
> > > > reading ours:
> > > >
> > > >
> > >
> >
>
http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/dcdplugin_8c.html
> > > >
> > > >
> > > > The source is available by CVS if you're
> > interested.
> > > >
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > >
> > > > On Thu, Mar 23, 2006 at 12:16:44AM +0800, Lin
> > wrote:
> > > > > Hi all,
> > > > >
> > > > > I am writing a dcd file reader, i can
> > successfully
> > > > read
> > > > > in the atoms into my system, however i am not
> > able to
> > > > > categorise the atoms into different
> > frames/timestep.
> > > > Does
> > > > > anyone has any idea why? Also, my simulation is
> > > > supposed
> > > > > to contain fixed atoms. However, after reading
> > the
> > > > > header, my nfixed atoms variable is found to be
> > 0.
> > > > Does
> > > > > anybody have any idea why? My dcd file is
> > generated
> > > > with
> > > > > NAMD Version 2.6b1.
> > > > >
> > > > > thanks a lot!
> > > > >
> > > > >
> > > > >
> > > > > __________________________________
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> > > > --
> > > > 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
> > > >
> > >
> > >
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> > --
> > 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
> >
>
>
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