Hi,
At the risk of sounding like a broken record this morning, I've
recently helped develop a protocol for preparing systems for
explicitly solvated MD that you may find useful:
https://aip.scitation.org/doi/abs/10.1063/5.0013849
I've also written a script that implements this protocol for Amber:
https://github.com/drroe/AmberMdPrep
Feel free to give it a try, it's still fairly rough around the edges,
so use with caution. Hope you find it useful!
-Dan
On Wed, Sep 23, 2020 at 7:47 AM Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> 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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> >
>
>
> --
>
> 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
> _______________________________________________
> AMBER mailing list
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Received on Wed Sep 23 2020 - 06:30:04 PDT
