AMBER Archive (2003)

Subject: AMBER: slower simulation

From: nie beining (nie_b_at_yahoo.com)
Date: Mon Sep 22 2003 - 10:43:24 CDT

  I ran 200ps MD simulation with protein fixed to equilibrate water molecules using belly command. The system contains 16,202 atoms. I am using sander of Amber 6 running simulations on single CPU of red hat linux cluster. 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? Or anyone had the same experience before? Many thanks!

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