Hi everyone,
I have a trajectory and velocity-trajectory file written by pmemd.cuda, and I’m interested in computing the kinetic energy at every frame, preferably using cpptraj. The values of ntwx and ntwv are set to the same number.
I want to do this because the kinetic energies that are written to “mdout” and “mden” do not correspond exactly to the written trajectory frames (i.e. mdout/mden are shifted by one frame with respect to the trajectory and velocity-trajectory). I need the kinetic energies that correspond exactly to my position trajectory frames, and it seems the only way to do this is to recompute them from the velocity-trajectory (please correct me if I’m wrong).
Looking through the cpptraj manual, I’m able to load in my velocities as coordinates; if I calculate the velocity squared for each atom, multiply by the atomic mass, and take the sum I should have my answer. I’m not entirely sure how to do this though.
Any feedback you have would be very helpful!
Thank you,
- Lee-Ping Wang
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Received on Mon Feb 12 2018 - 12:30:02 PST
