[gmx-users] trr file in VMD

[Justin A. Lemkul]

Paymon Pirzadeh wrote:
> Well,
> I would like to have each molecule's velocity magnitude in each frame
> (like an xtc file), and then watch it in VMD to see how different parts
> of a system will evolve in terms of their kinetics. Then, I think using
> the scale in the trajectory option of VMD, we might be able to see sth.
> no? 
> 
> 

Well, as Mark has just observed, velocity is a vector, so you won't be able to 
see it in VMD.  Plotting velocities with g_traj, combined with creative use of 
index groups and -b and -e options will give quantitative, and thus more easily 
communicated, results.

-Justin

> 
> On Sun, 2009-10-11 at 21:37 -0400, Justin A. Lemkul wrote:
>> 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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> 

-- 
========================================

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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