Re: [PyMOL] GROMACS Plugin

[Tomasz M. <to...@bi...>]

Hi Tsjerk,

Thank you for the tips about water-box. I have opened new issue and after
some verification I will most probably include it by default:
https://github.com/tomaszmakarewicz/Dynamics/issues/48

As it goes to "alternative protonation states", well GROMACS is big and
many of its functionalities are not yet implemented. At the moment pdb2gmx
adds protons to the molecule as it wants. There is now way to influence it
directly or indirectly (via pH) by the plugin. If you see this
functionality as an essential, please fill the issue on project GitHub
page:
https://github.com/tomaszmakarewicz/Dynamics/issues?state=open
I would also appreciate if together with issue, you will provide reference
GROMACS method of handling it. As far as I know, even GROMACS developers
are still scratching their heads, how to implement this:
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

Best regards,
-- 
Tomasz Makarewicz,
Laboratory of Biomolecular Systems Simulations,
Intercollegiate Faculty of Biotechnology,
University of Gdańsk and Medical University of Gdańsk,
Kładki 24, 80-822 Gdańsk, Poland

> Hi Tomasz,
>
> I think you don't need to explain to me how complex MD is :)
> My assumption is that your plugin is aimed primarily at simulations of a
> protein or so in solution, and cares to facilitate that. So, that sets the
> case. The main choice the user has is about the force field. That then
> determines most of the settings, as the electrostatics, etc, are
> essentially part of the force field. For the box, a rectangular unit cell
> is problematic if the solute rotates, so you shouldn't use that, even if
> it
> is the default. If the choice is then between a cubic and a rhombic
> dodecahedron, the latter is 71% of the size of the former, for whichever
> distance between images, so it will always be more efficient. The default
> size depends on what you put in. Thomas tried it on a heptapeptide, and it
> didn't work. In fact, as it is now, it wil only work out of the box for
> larger solutes. If you set a lower bound for the box size, it will also
> work for anything small.
>
> Out of curiosity, as I still have to try the plugin, how do you deal with
> alternative protonation states? Can you set them by clicking on the
> sequence? :)
>
> Cheers,
>
> Tsjerk
>
>
>
> On Thu, Aug 1, 2013 at 10:33 AM, Tomasz Makarewicz <
> to...@bi...> wrote:
>
>> Hi Tsjerk,
>>
>> It is not so easy to please all. If fact molecular dynamics simulation
>> is
>> so complex matter, that most setting should be set case by case. Plugin
>> manual describe how to deal with different options. As it goes to
>> waterbox, plugin is using default GROMACS options. Default size is
>> relative to molecule size and should work for most cases. The reason,
>> why
>> I did not increase it more by default, is that size of waterbox is most
>> important factor for calculation time. A little bigger waterbox,
>> increase
>> calculation time drastically.
>>
>> Best regards,
>> --
>> Tomasz Makarewicz,
>> Laboratory of Biomolecular Systems Simulations,
>> Intercollegiate Faculty of Biotechnology,
>> University of Gdańsk and Medical University of Gdańsk,
>> Kładki 24, 80-822 Gdańsk, Poland
>>
>> >  Hi Tomasz,
>> >
>> > Sure, the user can do it all, but the plugin is meant to take trouble
>> away
>> > from the user. Now you let the user run into some error, which does
>> not
>> > give a good hint how to solve the issue. If there is a standard
>> solution,
>> > which here is setting the box to some minimum allowable size, the
>> plugin
>> > should take care of it. The other point is about defaults, I would
>> have
>> > guessed the user can specify the box type, but the plugin, by default,
>> > should suggest the optimal one, which is a rhombic dodecahedron.
>> >
>> > Nice work though! :)
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> >
>> >
>> >
>> > On Thu, Aug 1, 2013 at 10:18 AM, Tomasz Makarewicz <
>> > to...@bi...> wrote:
>> >
>> >> Hi Tsjerk,
>> >>
>> >> Both size and shape of waterbox can be choose by GUI via plugin, by
>> >> clicking "Configure" under "Water Model" label in main plugin window.
>> >> Anyway, thanks for the tip.
>> >>
>> >> Best regards,
>> >> --
>> >> Tomasz Makarewicz,
>> >> Laboratory of Biomolecular Systems Simulations,
>> >> Intercollegiate Faculty of Biotechnology,
>> >> University of Gdańsk and Medical University of Gdańsk,
>> >> Kładki 24, 80-822 Gdańsk, Poland
>> >>
>> >>
>> >> > Hey :)
>> >> >
>> >> > I guess you tried the plugin with something quite small, using a
>> too
>> >> small
>> >> > distance between periodic images. This should be caught off by a
>> check
>> >> in
>> >> > the plugin, resetting the simulation cell if the usual criteria
>> result
>> >> in
>> >> > a
>> >> > too small one. The best way, IMHO, is checking the last line of the
>> >> .gro
>> >> > file obtained with editconf and replacing it by a 3.0 nm rhombic
>> >> > dodecahedron or cube. Not sure what the default box type is, but it
>> >> should
>> >> > be a rhombic dodecahedron :) I notice from the log that a
>> rectangular
>> >> cell
>> >> > was used.
>> >> >
>> >> > Cheers,
>> >> >
>> >> > Tsjerk
>> >> >
>> >> >
>> >> > On Thu, Aug 1, 2013 at 9:56 AM, Thomas Holder
>> >> > <tho...@sc...
>> >> >> wrote:
>> >> >
>> >> >> Hi Tomasz,
>> >> >>
>> >> >> Tomasz Makarewicz wrote, On 08/01/13 09:36:
>> >> >> > Thanks for the report. Could you send me file
>> >> >> > "~/.dynamics/NameOfMolecule/log.txt". It contains every GROMACS
>> >> >> output,
>> >> >> so
>> >> >> > we will be able to analyse, what exactly GROMACS is missing.
>> >> >>
>> >> >> The relevant error seems to be:
>> >> >>
>> >> >> ERROR 1 [file foo.top, line 710]:
>> >> >>   ERROR: The cut-off length is longer than half the shortest box
>> >> vector
>> >> >>   or longer than the smallest box diagonal element. Increase the
>> box
>> >> >>   size or decrease rlist.
>> >> >>
>> >> >> Full log:
>> >> >> http://pymol.org/tmp/dynamics-log.txt
>> >> >>
>> >> >> Cheers,
>> >> >>   Thomas
>> >> >>
>> >> >> --
>> >> >> Thomas Holder
>> >> >> PyMOL Developer
>> >> >> Schrödinger Contractor
>> >> >>
>> >> >>
>> >> >>
>> >>
>> ------------------------------------------------------------------------------
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>> >> >
>> >> >
>> >> > --
>> >> > Tsjerk A. Wassenaar, Ph.D.
>> >> >
>> >>
>> ------------------------------------------------------------------------------
>> >> > Get your SQL database under version control now!
>> >> > Version control is standard for application code, but databases
>> havent
>> >> > caught up. So what steps can you take to put your SQL databases
>> under
>> >> > version control? Why should you start doing it? Read more to find
>> out.
>> >> >
>> >>
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>> >>
>> >
>> >
>> > --
>> > Tsjerk A. Wassenaar, Ph.D.
>>
>>
>> -----------------------------------------
>> Ten list został wysłany z serwera Uniwersytetu Gdańskiego.
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>>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.


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