VMD-L Mailing List

From: Anil Kumar (anilk_at_jncasr.ac.in)
Date: Tue Dec 11 2007 - 21:00:58 CST

Hi Eddi,

I tried with the script you sent me but unfortunately it did not
work for me. First when I run the script it gave this error ::

_____________________________________
>Main< (N1000) 5 % source script.tcl

number of atoms is set to 1000
molecule 0: 1000 frames
setting user values for molecule 0
can't read "usr": no such variable
____________________________________

Then I modified a segment of script in this way

if { $name == "Na" } {
        set usr 0
        } else {
        set usr 1
        }

This time script run but still it is not changing the color.

Thanks
Anil

Eduard Schreiner said:
> Hi Anil,
>
> a script like the one below would do the job.
> Before I explain it, let me point some things:
>
> 1. This is a quick solution and there might be better ways to do that
> 2. The script needs an additional file containing all the names for every
> atom
> in every step, let's call it "allcrystalline.name" (actually I took the
> first column of the trajectory you sent and removed all "Atom" and "1000")
> 3. The script is not safe in the sense that it does not check, whether
> this additional name file is synchronous to the trajectory.
> 4. Might be there are some other drawbacks, but it works (at least for me)
>
>
> #=======================
> set molid 0
> set nr_atoms 1000
> #here I manually set these numbers
> puts "number of atoms is set to $nr_atoms"
>
> set nr_fr [molinfo $molid get numframes]
> puts "molecule $molid: $nr_fr frames"
>
> set fp [open "allcrystalline.name" r]
> #this is the additional file I told about
> puts "setting user values for molecule $molid"
>
> for {set j 0} {$j < $nr_fr} {incr j} {
> #going through the trajectory
> for {set i 0} {$i < $nr_atoms} {incr i} {
> set name [gets $fp]
> #here an entry from "allcrystalline.name" is read
> if { $name == "Na" } { set usr 0 } else {
> if { $name == "Ar" } { set usr 1 }
> }
> #and the variable usr is set depending on the name
> set sel [atomselect $molid "index $i" frame $j]
> #select the i'th atom in the current frame
> $sel set user $usr
> #set the user value for this atom
> $sel delete; unset sel
> }
> }
>
> unset j
> unset nr_fr
> unset fp
> unset i
> unset name
> unset nr_atoms
>
> #====================
>
> After you applied the above script, you can select the coloring according
> to
> the user value, or select the corresponding atoms directly .....
>
>
>
> Eddi
>
>
>
>
> On Tuesday 11 December 2007 11:20, Anil Kumar wrote:
>> Dear Eddi and all,
>>
>>
>> First, thank you for your reply. Yes I am using graphical interface and
>> I
>> checked it after activating the
>> 1. Update selection every frame
>> 2. Update color every frame.
>>
>> But unfortunately it did not work. I am attaching my trajectory file
>> with
>> this email and I would appreciate if any of you could solve this
>> problem.
>>
>> Thanks
>> Anil
>>
>> > > On Dec 11, 2007 2:06 PM, Eduard Schreiner <eduard.schreiner_at_rub.de >
>>
>> wrote:
>> > > > Hi Anil,
>> > > >
>> > > > I assume you are using the graphical interface.
>> > > > It sounds like the selection is not updated every frame.
>> > > > Thus, activate:
>> > > > "Update SelectionEvery Frame"
>> > > > and
>> > > > "Update Color Every Frame"
>> > > > for your selections in
>> > > > Graphics -> Representations -> Trajectory
>> > > >
>> > > >
>> > > > Hope this helps.
>> > > >
>> > > >
>> > > > Eddi
>> > > >
>> > > > On Tuesday 11 December 2007 05:43, Anil Kumar wrote:
>> > > > > Dear all,
>> > > > >
>> > > > > I want to make a movie, in VMD, of a trajectory(xyz coordinate
>> > > >
>> > > > file)
>> > > >
>> > > > > which is obtained from MC simulation. Trajectory file has two
>> type
>> > > >
>> > > > of
>> > > >
>> > > > > atoms (say A and B). Initial configuration has 10% of A atoms
>> and
>> > > >
>> > > > 90% of B
>> > > >
>> > > > > atoms. During the simulation number of A type atoms increases
>> and
>> > > >
>> > > > number
>> > > >
>> > > > > of B type atoms decreases. Final configuration has say 80% of A
>> and
>> > > >
>> > > > 20% of
>> > > >
>> > > > > B atoms.
>> > > > >
>> > > > > 1. Now I have given two elemental name for A and B atoms (say Ar
>> &
>> > > >
>> > > > Na).
>> > > >
>> > > > > When I visualize this file in VMD. Then color code it shows only
>> > > >
>> > > > from the
>> > > >
>> > > > > initial configuration(I mean 10% of particles have color A and
>> 90%
>> > > >
>> > > > of
>> > > >
>> > > > > particles have color B.) But it can't visualize the way the
>> number
>> > > >
>> > > > of A
>> > > >
>> > > > > particles have increased during simulation.
>> > > > >
>> > > > >
>> > > > > 2. Also, If I take only A type of Atoms in my trajectory file,
>> so
>> > > >
>> > > > this
>> > > >
>> > > > > trajectory file contains different number of Atoms in different
>> > > >
>> > > > frame(As
>> > > >
>> > > > > number of A type atoms increases during simulation). VMD can't
>> > > >
>> > > > visualize
>> > > >
>> > > > > this file.
>> > > > >
>> > > > > Could you please help me how to visualize above both type of
>> > > >
>> > > > trajectory
>> > > >
>> > > > > in VMD.
>> > > > >
>> > > > >
>> > > > > Thanking you in anticipation.
>> > > > >
>> > > > > With Best Regards,
>> > > > > Anil
>> > > > >
>> > > > >
>> > > > >
>> > > > >
>> > > > >
>> > > > > **************************
>> > > > > Anil Kumar
>> > > > > Research Scholar
>> > > > > Theoretical Sciences Unit
>> > > > > JNCASR, Bangalore
>> > > > > India -560064
>> > > > > Phone : 080-22082834
>> > > > > Mob. : 09342399856
>> > > > > Email:anilk_at_jncasr.ac.in
>> > > > > **************************
>> > > >
>> > > > --
>> > > >
>> > > > --
>> > > >
>> > > >
>> > > > =====================================================================
>> > > >========
>>
>> Eduard Schreiner e-mail:
>> > > > eduard.schreiner_at_theochem.rub.de
>> > > > Lehrstuhl fuer Theoretische Chemie Phone: ++49
>> > > > (0)234/32-22121
>> > > > Ruhr-Universitaet Bochum - NC 03/52 Fax: ++49
>> > > > (0)234/32-14045
>> > > > D-44780 Bochum
>> > > > http://www.theochem.rub.de
>> > > >
>> > > > =
>>
>> *************************
>> Anil Kumar,
>> Graduate Student,
>> Theoretical Sciences Unit,
>> JNCASR, Bangalore -560064
>> India
>> Phone : +91 80 2208 2834
>> ***************************
>
> --
>
> --
>
> =============================================================================
> Eduard Schreiner e-mail:
> eduard.schreiner_at_theochem.rub.de
> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-22121
> Ruhr-Universitaet Bochum - NC 03/52 Fax: ++49 (0)234/32-14045
> D-44780 Bochum http://www.theochem.rub.de
> =============================================================================
>

*************************
Anil Kumar,
Graduate Student,
Theoretical Sciences Unit,
JNCASR, Bangalore -560064
India
Phone : +91 80 2208 2834
***************************