Re: [AMBER] tutorials restructured and ConstpH/redox tutorial pages not accessible

From: Maria Nagan <>
Date: Wed, 23 Sep 2020 07:08:20 -0400

Dear Vaibhav,

Thanks for the email. Yes, we are in the process of restructuring with the following philosophy:
Make organization easier to read
Refer people to Tools outside of Amber.
Make new tutorials more modular.
Add Learning Outcomes to new tutorials.
Refer to literature and the Amber 2020 Manual.
I’m in the process this week of tweaking a few glitches (thanks for your patience).

Do you mean you would like an equilibration philosophy and protocol? Yes, two different people are working on this.

Thanks also for pointing out I’ll fix it. In the meantime, go here:

Specific to your system - is it explicit solvent? do you have restraints in your minimization? Are you slowly easing them off? Sometimes stepping down more gradually and interspersing with a little MD helps.

Maria Nagan
Chemistry Department
Stony Brook Univeristy
> On Sep 23, 2020, at 2:49 AM, Vaibhav Dixit <> wrote:
> Dear Amber developers/webmaster,
> I observed that the main-tutorial page has been restructured since I
> visited a couple of months ago. This is excellent as it looks more/better
> structured now.
> A great thanks to the Amber team.
> Are you considering to add another section useful for self-(re)training on
> the *basics of minimization, and heating steps*?
> Currently, after system setup/non-standard residue, there is a section
> directly on running MD.
> Please redirect me to the relevant tutorial if these are already discussed
> at length somewhere that I missed (I keep forgetting the imp of various
> options).
> I'm simulating a system where the E has not minimized even after 4-5 steps,
> the E as seen with mdout_analyzer keep getting lower. Thus I think I need a
> refresher in the basics, but I can't find such tutorial easily.
> Additionally, I'm unable to access the constant pH and Redox potential
> tutorial sections as shown below.
> Please redirect if there are new pages for the same.

> Thank you and best regards
> [image: image.png]
> --
> Regards,
> Dr. Vaibhav A. Dixit,
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email:,
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Received on Wed Sep 23 2020 - 04:30:02 PDT
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