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 <tomaszm@biotech.ug.gda.pl> 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
> <thomas.holder@schrodinger.com
>> 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!
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> 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.