[gmx-users] Questions about Visualization

[sabuj pattanayek]

Hi,

Actually UCSF Chimera may be easier in actually creating the animation.
After installing it you can use the Tools -> Molecular Dynamics -> Movie
plugin.

Then change the trajectory format to PDB, enter your first file (say
file1.pdb), and enter your last file (file10.pdb).


李 猛 wrote:
> 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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