AMBER Archive (2007)

Subject: AMBER: effective step period for constant pH simulations

From: Lillian chong (ltchong_at_pitt.edu)
Date: Mon Sep 24 2007 - 13:22:50 CDT

Hi,

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
residue..."

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
parameters?

Any clarification on this would be great.

Thanks!
Lillian

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