Re: [AMBER] Help: parameters of Equilibration and production scripts

From: Jason Swails <>
Date: Thu, 7 Jan 2016 06:59:45 -0500

On Thu, Jan 7, 2016 at 1:05 AM, Sehrish Naz <> wrote:

> 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.

​The manual explicitly describes each of these variables, and while parts
of the manual are surely unclear, the descriptions for these variables seem
clear to me.

Can you be more precise exactly what it is about the descriptions in the
manual you do not understand? Without knowing that, there is a good chance
my explanation would be similar to, if not the same as, what is put in the
manual and would be equally unhelpful. That would also help us possibly
improve the manual in the future.​


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jan 07 2016 - 04:00:04 PST
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