Hi Izwan,
First, you are never sure that you found the global minimum,
especially for very large molecules such biological ones. At least you
can check whether you got a local minimum or a local
maximum.
The best way to see if your system is equilibrated is to glance at the
energy vs time step. If the energy is fluctuating around a constant
value over the simulation, then the system is equilibrated. You can
check this by performing block averages of the energy.
Hope this help,
Pascal
izwan zainurul zainurulizwan80|-|yahoo.com wrote:
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Hai all,
I had done molecular dynamics to find
global minimum for cyclodextrin complex. I used Chem3D program to run
my molecular dynamics. How do I know I run simulation period
adequately? Thanks you.
- Izwan
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--
Dr. Pascal Boulet, Computational Chemist
University of Provence
Laboratoire Chimie Provence, UMR6264
Centre Saint-Jerome, case MADIREL
F-13397 MARSEILLE Cedex 20, France
Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11
courriel: pascal.boulet#%#univ-provence.fr
http://www.lc-provence.fr
http://allos.up.univ-mrs.fr/boulet
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