[gmx-users] Questions about Visualization

sabuj pattanayek sabuj.pattanayek at vanderbilt.edu
Thu Jun 2 02:57:01 CEST 2005


There are several programs that can do what you need: VMD
(http://www.ks.uiuc.edu/Research/vmd/), UCSF Chimera
(http://www.cgl.ucsf.edu/chimera/), and Pymol (http://pymol.sf.net). You
may need to convert your txt file format into a standard coordinate
format such as PDB (which itself is a simple txt file) or some other
format that these programs can understand. For example you could do
something like this:

HETATM    1 MG   MG  A   1     128.591  82.670  19.892  1.00  1.00

This would make a single (Mg) ion at x, y, z locations 128, 82, and 19.
Note that the spacing is important in PDB format (see

Hope that helps,
Sabuj Pattanayek
李 猛 wrote:
> Hi:
> I am a student in St.Francis Xavier University, Canada. I am sorry that 
> i am rude interrupting you by writing this email. I am a research 
> student this summer for Physics department of my university.
> I am looking for a visualization tool to simulate the movement of 
> spheres(actually moleculars), they collide with each other and then move 
> to another location in a certain box. The input data are locations of 
> spheres that generated by another program.
> Suppose there are 100 spheres in a box. The input data are 10 txt files 
> that include position (X, Y, Z) of each sphere at 10 different time. I 
> want to make an animation of the molecular according to the input files.
> Could you please give me some suggestion on the visualization tools (3D) 
> that take txt file as a input?  I am really appreciate your help!
>                                                             Meng Li
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