On Fri, Oct 07, 2011, Yun Shi wrote:
>
> Scaling up box by a factor of 1.300525 to meet diagonal cut criterion
>
> So what does the "scaling up" or "expansion" mean when using octahedral box?
I doubt that more than one or two people in the world know the answer, so
you will probably have to study the code. Maybe Bill Ross can chime in.
We should probably remove these "noisy" messages, since they just get in the
way of real communication to the users.
>
>
> Between this two solvation strategies, is it better to use the latter one
> since the density is more close to 1g/cc ?
The initial density is not relevant (but consider using a closeness parameter
of around 0.8, which helps.) For most biomolecules, the octahedral box is
better, since it is closer to a sphere, and fewer waters are needed to solvate
to a certain depth. Some types of simulations, such as membranes
or crystals, work better with other types of boundary models.
...good luck...dac
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Received on Fri Oct 07 2011 - 13:00:03 PDT
