[AMBER] Help: parameters of Equilibration and production scripts

From: Sehrish Naz <mjazse.gmail.com>
Date: Thu, 7 Jan 2016 11:05:43 +0500

Hi there,

I am working on small protein of 247 amino acids and having trouble in
running and understanding the equilibration scripts. (parameters such as
ntc, ntf, dt and noshakemask). I am not getting the correlation between
aforementioned parameters in parenthesis. Can anyone help me in
understanding the significance and correlation as well as how to prepare
the script. I am asking for help since amber tutorial and manual is not
clarifying my queries and concerns regarding shake parameters and its
correlation with dt.


* Sehrish Naz*

*Jr. Research Fellow,*

*Computational Chemistry Unit.*
*Dr. Panjwani Center for Molecular Medicine and Drug Research,*
*International Center for Chemical and Biological Sciences,*
*University of Karachi, Karachi-75270.*
*E-mail: mjazse.gmail.com <misbah.anwar88.gmail.com>*
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Received on Wed Jan 06 2016 - 22:30:04 PST
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