[gmx-users] trr file in VMD

[Justin A. Lemkul]

Paymon Pirzadeh wrote:
> I did that but, it did not work! I just get a constant color.
> 

Unless the velocity is written to a field that VMD recognizes, I don't think 
you'll be able to see the velocities colored.  For example, VMD can color by 
B-factor or occupancy, neither of which would be useful for velocities, because 
I don't know of a way to write velocity information to these fields.

You can plot velocities using g_traj -ov, but without knowing what you're trying 
to do, then it's hard to provide anything else.

-Justin

> 
> 
> On Sun, 2009-10-11 at 18:27 -0700, Amit Choubey wrote:
>> yes you can do that by opening the gro file and then loading the .trr
>> file .
>>
>> amit
>>
>> On Sun, Oct 11, 2009 at 6:22 PM, Paymon Pirzadeh
>> <ppirzade at ucalgary.ca> wrote:
>>         Hello,
>>         How can we use the trr file in VMD? I thought since we ask in
>>         the mdp
>>         file to output the velocities, then in VMD we should be able
>>         to see
>>         molecules colored based on their velocities through the
>>         trajectory
>>         options. Am I correct?
>>         
>>         Payman
>>         
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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