[gmx-users] Re: Minimum simulation time needed to have a completely minimized structure

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 10 16:23:41 CET 2010

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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