[gmx-users] trr file in VMD

[Paymon Pirzadeh]

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? 



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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