VMD-L Mailing List

From: Anil Kumar (anilk_at_jncasr.ac.in)
Date: Wed Dec 12 2007 - 01:48:06 CST

Thanks Axel for suggestions, I am trying the way you have suggested and let
you know if it works.

Anil

On Dec 12, 2007 9:20 AM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:

> On Wed, 12 Dec 2007, Anil Kumar wrote:
>
> anil,
>
> it won't work "black box" style. your problem is almost orthogonal
> to what VMD was written for. if you didn't notice
> eddi's idea (which is equivalent to what i already suggested
> before without going into detail) here some more explanations.
>
> you have to first read in your trajectory (pre-requisite
> the total number of atoms does not change). now VMD assumes,
> that atom names do not change over the course of a trajectory,
> so after the first frame, it will only read the coordinates.
>
> now you can store a single property, per frame and per atom
> in the user field, but you have to write a (tcl) script that
> reads the whole trajectory file and for each frames encodes
> the atom type - as eddi suggested - as numbers 1,2,... and
> so on. example 5.3 and 5.4 at:
>
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect3>
> have an example on how you can store a property in the user
> field and read data from an external file. you'll have to
> merge this and adapt it for your purposes.
>
> finally, you have the option to visualize the result either
> by using the User colorization or building multiple representations
> where you use selections of the kind "user == 1" , "user == 2"
> and pick the appropriate color for each of the atom types.
> of course, that requires activating the "update color" flag
> in the first and "update selection" flag in the second case.
>
> hope that helps,
> axel.
> AK>
> AK> Hi Eddi,
> AK>
> AK> I tried with the script you sent me but unfortunately it did not
> AK> work for me. First when I run the script it gave this error ::
> AK>
> AK> _____________________________________
> AK> >Main< (N1000) 5 % source script.tcl
> AK>
> AK> number of atoms is set to 1000
> AK> molecule 0: 1000 frames
> AK> setting user values for molecule 0
> AK> can't read "usr": no such variable
> AK> ____________________________________
> AK>
> AK> Then I modified a segment of script in this way
> AK>
> AK> if { $name == "Na" } {
> AK> set usr 0
> AK> } else {
> AK> set usr 1
> AK> }
> AK>
> AK> This time script run but still it is not changing the color.
> AK>
> AK>
> AK> Thanks
> AK> Anil
> AK>
> AK>
> AK>
> AK>
> AK>
> AK>
> AK>
> AK> Eduard Schreiner said:
> AK> > Hi Anil,
> AK> >
> AK> > a script like the one below would do the job.
> AK> > Before I explain it, let me point some things:
> AK> >
> AK> > 1. This is a quick solution and there might be better ways to do
> that
> AK> > 2. The script needs an additional file containing all the names for
> every
> AK> > atom
> AK> > in every step, let's call it "allcrystalline.name" (actually I took
> the
> AK> > first column of the trajectory you sent and removed all "Atom" and
> "1000")
> AK> > 3. The script is not safe in the sense that it does not check,
> whether
> AK> > this additional name file is synchronous to the trajectory.
> AK> > 4. Might be there are some other drawbacks, but it works (at least
> for me)
> AK> >
> AK> >
> AK> > #=======================
> AK> > set molid 0
> AK> > set nr_atoms 1000
> AK> > #here I manually set these numbers
> AK> > puts "number of atoms is set to $nr_atoms"
> AK> >
> AK> > set nr_fr [molinfo $molid get numframes]
> AK> > puts "molecule $molid: $nr_fr frames"
> AK> >
> AK> > set fp [open "allcrystalline.name" r]
> AK> > #this is the additional file I told about
> AK> > puts "setting user values for molecule $molid"
> AK> >
> AK> > for {set j 0} {$j < $nr_fr} {incr j} {
> AK> > #going through the trajectory
> AK> > for {set i 0} {$i < $nr_atoms} {incr i} {
> AK> > set name [gets $fp]
> AK> > #here an entry from "allcrystalline.name" is read
> AK> > if { $name == "Na" } { set usr 0 } else {
> AK> > if { $name == "Ar" } { set usr 1 }
> AK> > }
> AK> > #and the variable usr is set depending on the name
> AK> > set sel [atomselect $molid "index $i" frame $j]
> AK> > #select the i'th atom in the current frame
> AK> > $sel set user $usr
> AK> > #set the user value for this atom
> AK> > $sel delete; unset sel
> AK> > }
> AK> > }
> AK> >
> AK> > unset j
> AK> > unset nr_fr
> AK> > unset fp
> AK> > unset i
> AK> > unset name
> AK> > unset nr_atoms
> AK> >
> AK> > #====================
> AK> >
> AK> > After you applied the above script, you can select the coloring
> according
> AK> > to
> AK> > the user value, or select the corresponding atoms directly .....
> AK> >
> AK> >
> AK> >
> AK> > Eddi
> AK> >
> AK> >
> AK> >
> AK> >
> AK> > On Tuesday 11 December 2007 11:20, Anil Kumar wrote:
> AK> >> Dear Eddi and all,
> AK> >>
> AK> >>
> AK> >> First, thank you for your reply. Yes I am using graphical
> interface and
> AK> >> I
> AK> >> checked it after activating the
> AK> >> 1. Update selection every frame
> AK> >> 2. Update color every frame.
> AK> >>
> AK> >> But unfortunately it did not work. I am attaching my trajectory
> file
> AK> >> with
> AK> >> this email and I would appreciate if any of you could solve this
> AK> >> problem.
> AK> >>
> AK> >> Thanks
> AK> >> Anil
> AK> >>
> AK> >> > > On Dec 11, 2007 2:06 PM, Eduard Schreiner <
> eduard.schreiner_at_rub.de >
> AK> >>
> AK> >> wrote:
> AK> >> > > > Hi Anil,
> AK> >> > > >
> AK> >> > > > I assume you are using the graphical interface.
> AK> >> > > > It sounds like the selection is not updated every frame.
> AK> >> > > > Thus, activate:
> AK> >> > > > "Update SelectionEvery Frame"
> AK> >> > > > and
> AK> >> > > > "Update Color Every Frame"
> AK> >> > > > for your selections in
> AK> >> > > > Graphics -> Representations -> Trajectory
> AK> >> > > >
> AK> >> > > >
> AK> >> > > > Hope this helps.
> AK> >> > > >
> AK> >> > > >
> AK> >> > > > Eddi
> AK> >> > > >
> AK> >> > > > On Tuesday 11 December 2007 05:43, Anil Kumar wrote:
> AK> >> > > > > Dear all,
> AK> >> > > > >
> AK> >> > > > > I want to make a movie, in VMD, of a trajectory(xyz
> coordinate
> AK> >> > > >
> AK> >> > > > file)
> AK> >> > > >
> AK> >> > > > > which is obtained from MC simulation. Trajectory file has
> two
> AK> >> type
> AK> >> > > >
> AK> >> > > > of
> AK> >> > > >
> AK> >> > > > > atoms (say A and B). Initial configuration has 10% of A
> atoms
> AK> >> and
> AK> >> > > >
> AK> >> > > > 90% of B
> AK> >> > > >
> AK> >> > > > > atoms. During the simulation number of A type atoms
> increases
> AK> >> and
> AK> >> > > >
> AK> >> > > > number
> AK> >> > > >
> AK> >> > > > > of B type atoms decreases. Final configuration has say 80%
> of A
> AK> >> and
> AK> >> > > >
> AK> >> > > > 20% of
> AK> >> > > >
> AK> >> > > > > B atoms.
> AK> >> > > > >
> AK> >> > > > > 1. Now I have given two elemental name for A and B atoms
> (say Ar
> AK> >> &
> AK> >> > > >
> AK> >> > > > Na).
> AK> >> > > >
> AK> >> > > > > When I visualize this file in VMD. Then color code it shows
> only
> AK> >> > > >
> AK> >> > > > from the
> AK> >> > > >
> AK> >> > > > > initial configuration(I mean 10% of particles have color A
> and
> AK> >> 90%
> AK> >> > > >
> AK> >> > > > of
> AK> >> > > >
> AK> >> > > > > particles have color B.) But it can't visualize the way the
> AK> >> number
> AK> >> > > >
> AK> >> > > > of A
> AK> >> > > >
> AK> >> > > > > particles have increased during simulation.
> AK> >> > > > >
> AK> >> > > > >
> AK> >> > > > > 2. Also, If I take only A type of Atoms in my trajectory
> file,
> AK> >> so
> AK> >> > > >
> AK> >> > > > this
> AK> >> > > >
> AK> >> > > > > trajectory file contains different number of Atoms in
> different
> AK> >> > > >
> AK> >> > > > frame(As
> AK> >> > > >
> AK> >> > > > > number of A type atoms increases during simulation). VMD
> can't
> AK> >> > > >
> AK> >> > > > visualize
> AK> >> > > >
> AK> >> > > > > this file.
> AK> >> > > > >
> AK> >> > > > > Could you please help me how to visualize above both type
> of
> AK> >> > > >
> AK> >> > > > trajectory
> AK> >> > > >
> AK> >> > > > > in VMD.
> AK> >> > > > >
> AK> >> > > > >
> AK> >> > > > > Thanking you in anticipation.
> AK> >> > > > >
> AK> >> > > > > With Best Regards,
> AK> >> > > > > Anil
> AK> >> > > > >
> AK> >> > > > >
> AK> >> > > > >
> AK> >> > > > >
> AK> >> > > > >
> AK> >> > > > > **************************
> AK> >> > > > > Anil Kumar
> AK> >> > > > > Research Scholar
> AK> >> > > > > Theoretical Sciences Unit
> AK> >> > > > > JNCASR, Bangalore
> AK> >> > > > > India -560064
> AK> >> > > > > Phone : 080-22082834
> AK> >> > > > > Mob. : 09342399856
> AK> >> > > > > Email:anilk_at_jncasr.ac.in
> AK> >> > > > > **************************
> AK> >> > > >
> AK> >> > > > --
> AK> >> > > >
> AK> >> > > > --
> AK> >> > > >
> AK> >> > > >
> AK> >> > > >
> =====================================================================
> AK> >> > > >========
> AK> >>
> AK> >> Eduard Schreiner e-mail:
> AK> >> > > > eduard.schreiner_at_theochem.rub.de
> AK> >> > > > Lehrstuhl fuer Theoretische Chemie Phone: ++49
> AK> >> > > > (0)234/32-22121
> AK> >> > > > Ruhr-Universitaet Bochum - NC 03/52 Fax: ++49
> AK> >> > > > (0)234/32-14045
> AK> >> > > > D-44780 Bochum
> AK> >> > > > http://www.theochem.rub.de
> AK> >> > > >
> AK> >> > > > =
> AK> >>
> AK> >> *************************
> AK> >> Anil Kumar,
> AK> >> Graduate Student,
> AK> >> Theoretical Sciences Unit,
> AK> >> JNCASR, Bangalore -560064
> AK> >> India
> AK> >> Phone : +91 80 2208 2834
> AK> >> ***************************
> AK> >
> AK> > --
> AK> >
> AK> > --
> AK> >
> AK> >
> =============================================================================
> AK> > Eduard Schreiner e-mail:
> AK> > eduard.schreiner_at_theochem.rub.de
> AK> > Lehrstuhl fuer Theoretische Chemie Phone: ++49
> (0)234/32-22121
> AK> > Ruhr-Universitaet Bochum - NC 03/52 Fax: ++49
> (0)234/32-14045
> AK> > D-44780 Bochum
> http://www.theochem.rub.de
> AK> >
> =============================================================================
> AK> >
> AK>
> AK>
> AK> *************************
> AK> Anil Kumar,
> AK> Graduate Student,
> AK> Theoretical Sciences Unit,
> AK> JNCASR, Bangalore -560064
> AK> India
> AK> Phone : +91 80 2208 2834
> AK> ***************************
> AK>
>
> --
> =======================================================================
> 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.
> 

-- 
Anil Kumar
Research Scholar,
Theoretical Sciences Unit,
JNCASR, Bangalore,
India, 560064
Email: anilk_at_jncasr.ac.in
Phone: +91 80 2208 2928