[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 archananiper@gmail.com To: modeller-care@salilab.org
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?
> can anybody tellm e more details about molecular dynamic simulations > performed in modeller.
See http://salilab.org/modeller/9v1/manual/node373.html
> 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
It will probably take about 10-30 minutes. The easiest way to find out is to run it...
> what is time requirement if i use SGI, IRIX > 6.5 fuel work station for the same using default parameters in modeller?
An SGI IRIX box is probably about 10 times slower than a modern PC.
> 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?
The default Modeller procedure is to take the final model, and we find that works well.
Ben Webb, Modeller Caretaker
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Modeller Caretaker