You both may be interested in the program "packmol" which was written
specifically with this kind of task in mind. Of course, you know Manuel's
approach works, since he's used it himself :).
All the best,
Jason
On Mon, Feb 2, 2015 at 6:36 PM, <mmaestre.gate.sinica.edu.tw> wrote:
> Hi Said,
>
>
> one way in which I've added high concentrations of a solute into a box,
> with fine control over concentration, is by using the addtobox program,
> which is normally used for preparing in-crystal simulations. Then,
> following the in crystal simulation procedure, I add different amounts of
> water and run short constant pressure simulations until I get a box volume
> in which the number of included solutes corresponds to the desired
> concentration.
> Check the crystal simulation tutorial for more information!
>
> http://ambermd.org/tutorials/advanced/tutorial13/XtalTutor1.html
>
> I'm sure there are other, more elegant, ways, and I'm sure people that
> know better than me will be able to tell you about them, but this one
> worked for me.
>
> Hoping it helps,
> Manuel
>
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Feb 02 2015 - 17:30:02 PST
