AMBER Archive (2004)

Subject: RE: AMBER: MD simulation : problem

From: sachin patil (sachin_ppatil_at_yahoo.com)
Date: Sun Jul 11 2004 - 10:08:13 CDT

Hi Ross,
 Thank you for you suggestions. It really helps a lot.
 Actually, I have solvated my system with a water cap (32 water residues) and I am trying to see the movement of the water molecules.
 I tried to run the simulation with periodic boubdary conditions (cutoff 12.0) but the system just doesn't go anywhere. So I switched to nonperiodic conditions as mentioned
 in the Streptavidin Biotin tutorial.
 But my problem was that I was not sure whether I am correct in using non-periodic
 conditions for my system.
  So my questions is how do one selectes whether he should use periodic or non-periodic conditions for his system?
 
Thank you again
 
Regards
Sachin Patil
-----------------
Dept. of Medicinal & Biological Chemistry
University of Toledo, Toledo
Ohio 43606

                
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