VMD-L Mailing List

From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
Date: Mon Oct 23 2000 - 11:55:02 CDT

Hello,

On Mon, Oct 23, 2000 at 03:38:14PM +0200, Grzegorz Bakalarski wrote:
> Hello,
>
> I look for a graphical program to visualize MD. The program should be as simple
> as possible. It is for my students that write their first MD code. The input
> should be as simple as possible ,eg.
> atom_type, x,y,z
>
> for some 1000 steps, system consists of max 1000 atoms. It would be nice if it could color
> atoms using kinetic energy, but this is not very important. It does not have to have advanced graphics -
> spheres or crosses would be OK. It has to run on SGI Indy IRIX 6.2 R4400 old machine.
> It should also be for free ...
> I tested VMD and MOIL-VIEW, however they are to complex (and I don't know AMBER
> trajectory format). It just should show my student the behavior of system.

        I use VMD quite a bit (its developed in my research group).
It has many advanced features, but don't be scared off, VMD really
isn't 'too complex' for this application, there's not a giant learning
curve required for what you want to do. VMD can read plain ASCII text
files, in the popular PDB format. An output procedure that writes x,
y, z coordinates to a file can be changed to write in the PDB 'ATOM'
record format. VMD can input multiple PDB files and make a
trajectory from them. This process can be automated with a four line
TCL script. Your students would just have to output numbered files
numbered, for example, 00001.pdb through 01000.pdb,

        For instance, to load files 'frame-00001.pdb' through
'frame-00150.pdb' you'd type this into the command line after starting
up vmd...

mol load pdb 00001.pdb
for {set i 2} {$i<=150} {incr i} {
        set fileName [format frame-%05.0f.pdb $i]
        animate read pdb $fileName
}

        And you're done: now press 'Animate' in the main menu to bring
up the 'Animate' dialog box, and press the VCR-like buttons in the
'Animate' dialog box to animate the trajectory. A little bit more TCL
scripting can make the colors of every atom change every time step to
track KE (or anything else you'd like). (Note that I didn't mention the
AMBER trajectory format once!)

        Now for just just a little more relentless plugging:

 VMD is free, runs on SGI machines, and many other architectures (Sun,
HP, etc., plus Linux PC's and Windows PC's.) It's under current
development, with an active user and developer bases. More details,
and full documentation, downloads, and source code on the web site....
        
http://www.ks.uiuc.edu/Research/vmd/

                                        Cheers,

                                        Barry 

-- 
Barry Isralewitz     Beckman 3121    Theoretical Biophysics Group, UIUC  
Office Phone: (217) 244-1612    Home Phone: (217) 337-6364
email: barryi_at_ks.uiuc.edu      http://www.ks.uiuc.edu/~barryi