AMBER Archive (2007)

Subject: AMBER: How to modify the velocity of a water molecule?

From: Ji-Lai Li (jlutcc_at_gmail.com)
Date: Thu Feb 15 2007 - 20:15:45 CST

Dear Amber Users:
  I am doing targeted md. My protein is solvated by a shell of water. The
whole has been equilibrated. When the TMD runs for a period of time,
sometimes 300 ps, or 500ps, there is a water molecule escapes from the
surface. It is headachy.
  Now, I want to modify the velocity of the escaping water, and let it run
to the opposite direction. I think it is physical. Correct? If yes, how to
modify it form the *.rst file?
  Is there someone know the realy meaning of the RST file?

Ji-Lai Li

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu