[MMTK] pdb full simulation

mprabha@fiu.edu mprabha at fiu.edu
Tue Jan 24 17:53:30 CET 2006


thank you for the information
can you specify pair calculation interval.
The simulation for 1CF (protein alone) runs smoothly.
It takes 55 minutes of a linux  computer (red hat 8.0)
with 10.0 A cutoff for non bonded interactions.and multipole electrostatics.
for 1 ps. If any body needs,  i can forward the entire steps
1) amber force field parametrization & topology buildup
2) hydrogen addition
3) minimization 
4) heating & equilibration
5) production run
6) restart information
7) visulization8) trajectory analysis using xMoldynwith solvent addition is 
possible. But computer time needed is very high.

thank you
prabha karan




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