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[modeller_usage] [Fwd: molecular dynamics simulations in modeller]



-------- Original Message --------
Subject: 	molecular dynamics simulations in modeller
Date: 	Wed, 28 Mar 2007 16:46:38 +0530
From: 	Archana Chavan <>
To: 	



hello,
can anybody tellm e more details about molecular dynamic simulations
performed in modeller.
i am using modeller 8v2 version on pentium IV workstation
so how much time it may take to optimize the protein containing
two chains, having length of 423 amino acid residues on the workstation
i am using currently, and what is time requirement if i use SGI, IRIX
6.5 fuel work station for the same using default parameters in modeller?

another thing i want to know is, which is the preferred method to obtain
the best result after MD, whether i should go for the final model after
all the steps of MD or the least energy model out of all the possible
conformations it generated?


--
Archana Chavan
MS (Pharm)Pharmacoinformatics
National Institute of Pharmaceutical Education and Research (NIPER)
Mohali-160 062
Punjab, India.


	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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