[gmx-users] Questions about Visualization

[李 猛]

Hi:
 Thanks for your reply!
 I have learned VMD by myself for two weeks, I am the only first one in my 
group who use VMD, so I can not find any other people to help me. I just 
know some basic operations of it, Could you please help me out on how to 
make an animation from the 10 PDB input files?
 Is it right that I load the 10 PDB files together?
                                                                            

                                                                           
Sincerely
                                                                            
 Meng Li 

>From: sabuj pattanayek <sabuj.pattanayek at vanderbilt.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Questions about Visualization
>Date: Wed, 01 Jun 2005 19:57:01 -0500
>
>Hi,
>
>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
>http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_2.html).
>
>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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