AMBER: effective step period for constant pH simulations

From: Lillian chong <>
Date: Mon, 24 Sep 2007 14:22:50 -0400


I'm confused about the following statement in the AMBER9 manual under
"Running at constant pH": "...Note that only one residue is examine on each
step, so you should decrease the step period as the number of titrating
residues increases to maintain a constant effective step period for each

What is meant by the "effective step period"? From what I understand, when
you specify ntcnstph=5 and dt=0.002, this means that there are 10 fs of MD
simulation between MC steps. The manual mentions that good results have
been obtained with a 100 fs effective step period for each residue (e.g.
ntcnstph=5, dt=0.002 with about 10 residues titrating). Not sure how an
effective step period of 100 fs per residue is concluded from these

Any clarification on this would be great.


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Received on Wed Sep 26 2007 - 06:07:03 PDT
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