AMBER: slow simulation

From: nie beining <>
Date: Sun, 21 Sep 2003 23:46:21 -0700 (PDT)

      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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Received on Mon Sep 22 2003 - 07:53:00 PDT
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