RE: AMBER: MD simulation : problem

From: sachin patil <>
Date: Sun, 11 Jul 2004 08:08:13 -0700 (PDT)

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
Sachin Patil
Dept. of Medicinal & Biological Chemistry
University of Toledo, Toledo
Ohio 43606

Do you Yahoo!?
Yahoo! Mail is new and improved - Check it out!
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jul 11 2004 - 16:53:01 PDT
Custom Search