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
<ppirz...@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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