With reference to the above tutorial in in particular Section 2 (
http://ambermd.org/tutorials/advanced/tutorial3/section2.htm), it is stated that "We will check this in the same fashion as we did for the last equilibration step by plotting the density, temperature, total energy"
It is not clear to me how can this be done. In the equilibration step the script proces_mdout.pl uses as inputs heat.out, density.out and equil.out. In the production simulation there are no heat.out and density.out files.
Any explanation on this would be most welcome.
Best regards
George
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Received on Thu Aug 05 2010 - 10:00:03 PDT
