AMBER Archive (2003)

Subject: AMBER: slow simulation

From: nie beining (nie_b_at_yahoo.com)
Date: Mon Sep 22 2003 - 01:46:21 CDT

      I ran 200ps MD simulation with protein fixed to equilibrate water molecules. I found that coordinates were printed out 3ps/hr after I used the restart coordinates to run simulation allowing everything to move. The simulation without equilibrating water was printing coordinates at 7ps/hr. I am a pretty new user. Is there any reason for slower printing out? How to improve the speed of simulation without changing any control parameters? Thanks!
 

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