Dear Daniel,
Thanks for sharing this.
I will try this asap tomorrow and let you know if I have any questions.
Cheers
On Wed, Sep 23, 2020, 18:57 Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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>_______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> >
> > 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 23 2020 - 08:30:02 PDT
