AMBER Archive (2007)

Subject: Re: AMBER: effective step period for constant pH simulations

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Mon Sep 24 2007 - 13:31:05 CDT

Lilian,

indeed, there are 10 fs between MC steps, but since ONLY one is looked
at every MC step, with 10 residues being protonable, each one is really
looked at ONLY after 100 fs, on average.

Makes sense ?

Lillian chong wrote:
> 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
> 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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