> 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