Kinetic Energy difference using restart binaries

From: Mikolai Fajer (
Date: Wed Dec 21 2005 - 12:54:13 CST

    I ran a short (50 ps) MD in order to equilibrate my system. I
then took the binary restart files to run a longer MD. I used the
following input parameters for the longer MD run:

structure ../common/build_wb.psf
coordinates ../common/build_wb.pdb
bincoordinates ../common/build_wb_eq.coor
binvelocities ../common/build_wb_eq.vel
extendedSystem ../common/build_wb_eq.xst

    The kinetic energies of the two MD are drastically different, both
at the area around the restart as well as on average. The average
potential of the first MD is 16731 kcal/mol, and of the second MD is
11483 kcal/mol. Where is this difference coming from?

     -Mikolai Fajer-

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