Dear Maria and Amber developers,
Thanks for helping me understand your philosophy used in reorganizing the
Amber tutorial. I'm sure it will help the community immensely.
I can see a page where heating and equilibration are being explained (I'll
read that).
http://ambermd.org/tutorials/basic/tutorial13/index.php
If possible please add a separate sub-section before this on minimization
of representative nucleic acid, proteins and lipids or even combination of
such systems. A general (brief) guide on using various min/heat/equil
input file options will be really valuable. I wish if there can be a page
for major keywords similar to available in other software like Gaussian.
These could be divided into sander/pmemd jobs type (min/heat/equil) and/or
advanced MD methods. I understand that this can become a daunting task
considering a large number of options and their combinations available with
Amber/AmberTools programs. Nevertheless, I'm hoping that you can try to
cover the most basic and common keyword options central to MD.
Regarding my particular case, I'm working on it using older input files,
messages on archive and the manual. I'll get back to the list if I face
problems.
I hope this helps you.
Thank you very much and best regards.
On Wed, Sep 23, 2020 at 4:38 PM Maria Nagan <maria.c.nagan.gmail.com> wrote:
> 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
> http://ambermd.org/tutorials/advanced/tutorial33/section1.htm. I’ll fix
> it. In the meantime, go here:
> http://ambermd.org/tutorials/advanced/tutorial33/index.htm
> http://ambermd.org/tutorials/advanced/tutorial33/section1.htm
> http://ambermd.org/tutorials/advanced/tutorial33/section2.htm
> http://ambermd.org/tutorials/advanced/tutorial33/section3.htm
> http://ambermd.org/tutorials/advanced/tutorial33/section4.htm
>
> 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
> ==========
> Maria Nagan
> Chemistry Department
> Stony Brook Univeristy
> > On Sep 23, 2020, at 2:49 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
> 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.
> > http://ambermd.org/tutorials/advanced/tutorial33/section1.php
> > 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: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >
> > ORCID ID: https://orcid.org/0000-0003-4015-2941
> >
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >
> > P Please consider the environment before printing this e-mail
> > <image.png>_______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
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>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
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: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
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Received on Wed Sep 23 2020 - 05:00:02 PDT
