[gmx-users] trr file in VMD
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 12 03:37:02 CEST 2009
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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