Yanmei Song wrote:
Dear Users:
I am in the process of setting up a new system. I have a 8.0*8.0*8.0
nm3 system which include 27800 molecules. When the system approach
equilibrium, I found the potential energy is +3e5 (big positive number).
Is this normal? Since based on my experience, for systems in such size,
the potential energy is usually a big negative number? Does this mean
that my force field parameter or molecule structure have problems?
Thanks in advance!
A positive potential indicates repulsive interaction(s) is (are) present in your
system, i.e. you have clashes or have faulty parameters. Energy minimization
should converge to a nice, negative number.
-Justin
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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