[gmx-users] trr file in VMD

[Mark Abraham]

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.

Now that I stop and think about it... velocity is a vector... how did 
the original poster want to colour by a vector? Speed would be a 
different matter (but nearly useless). Usually you'd have to use an 
arrow to represent velocity, and ordinarily the length of the arrow 
would be better way to indicate the speed than the colour of 
fixed-length arrows.

Mark

> 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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>