Re difference in total energy values

From: Boyang Wang (
Date: Wed Mar 15 2006 - 15:44:33 CST

Hi. Just to ask if you have the 1-4 scaling parameter, Langevin dynamics and other simulation details exactly the same when you run the simulation and when you use MDenergy. Did you average over many frames?
Osman Yogurtcu <> Hi,
  Recently, I calculated and compared the total energy values (per frame) of a NAMD simulation both with NAMDDAT and MDenergy. The values are not even close. Does anybody know the reason why this might be the case?
  Osman N. Yogurtcu
  Center for Computational Biology and Bioinformatics
Research Assistant
Koc University

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