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 functionali
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
determi
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
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
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 Biotechn
Hi Thomas,
That's pretty easy. Water-box is just too small. You can increase the
water-box size by pressing "Configure" in the main plugin window under the
"Water Model" label.
Best regards,
--
Tomasz Makarewicz,
Laboratory of Biomolecular Systems Simulations,
Intercollegiate Faculty of Biotechno
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 th
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
Hi Thomas,
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.
You should also not remove those two lines of code. This is the part of
code, which in case of such an e
