[gmx-users] Difference between kinetic energy from .xvg file and calculated kinetic energy from velocities

Samantha Sanders sasander at princeton.edu
Sat Mar 27 03:57:33 CET 2010


            I have run a simulation and using g_energy on the .edr file, I
have been looking at the kinetic energies in the resulting .xvg file.  It is
my understanding that these are the instantaneous kinetic energies for those
times.  However, when I try to calculate the kinetic energy on my own using
the frames from my trajectory file and being sure to compare the same
timestamps of the trajectory and the .edr file, I am not getting the same
values for the kinetic energy.  My first question is should I get the same
values between the two sources: the .xvg file and the velocities in the
frames of my trajectory file?  If so, any suggestions for why I may not be
getting the same values or if there are any other adjustments I should make?
I have simply been calculating the kinetic energy as the sum of .5mv^2 for
all particles.  I have read the manual and the various mailing list
responses and I am still unsure about this.  There may be something simple I
am missing.  Any help is appreciated.   Thank you!




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