bharat gupta wrote:
Hi all
I wanna know that for how long shall I run the energy minimization
step to minimize my modelled protein structure .. and what all
parameters shall I look for the minimized structure - rms , rmsf ,
potential , g_energy . In g_energy total energy and potential both
have to be checked ...
You probably won't get much in the way of RMSD or RMSF during EM; the structure
shouldn't be changing drastically. Convergence of EM is usually judged based on
the magnitude of Fmax and the potential (printed by mdrun at the end of EM).
There is no total energy term during EM. Since there is no kinetic energy, the
total energy and potential energy are the same. If you run g_energy on the .edr
file, you'll see for yourself :)
-Justin
--
========================================
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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