From: E. Prabhu Raman (eraman_at_gmu.edu)
Date: Fri Sep 29 2006 - 13:39:55 CDT
When I try to extend my simulation by using the following lines in my configuration file:
# input system......
structure CGMrealunits.psf # OK
coordinates ./output/CGM001.coor #final coors from first run
bincoordinates ./output/CGM001i.coor #final bin coordinates from first run
binvelocities ./output/CGM001i.vel $final velocities from 1st run
I come across an artifact: The energies (as obtained from the redirected stdout) from the last step of the first run, do not exactly match with those of the step# zero of the second run. The energy records are pasted below.
ENERGY: 35000000 19.8583 11.8583 2.7822 10.1637 0.0000 -53.8806 0.0000 0.0000 47.8905 38.6724 349.2695 38.6031 38.7933 349.4812
ENERGY: 0 19.8579 11.8584 2.7822 10.1636 0.0000 -53.8805 0.0000 0.0000 47.2771 38.0587 344.7962 38.0606 38.0606 344.7962
I am using Langevin dynamics with a temperature of 348K ( I do not specify any initial temperature in the second run as I am importing velocities from the 1st).
Any idea why is there a differece in energies?
Thanks in advance
Ph.D Student,Bioinformatics & Computational Biology
George Mason University
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