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#1184 - 04/02/04 01:06 PM RHDO water box
dmr Offline
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Registered: 04/02/04
Posts: 9
Loc: University of Wisconsin, Madis...
Does anyone have a fast solution to making a RHDO water box, with a=35 or so?

Thankyou in advance for your help.

Demian

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#1185 - 04/03/04 05:51 PM Re: RHDO water box [Re: dmr]
rmv Online   content

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
I recently made an RHDO of water with A=36, and have posted my script to the archive.

In brief, I create a sphere with the same volume (and therefore number of water molecules) by cutting a spherical octant (1/8th) from a box and rotating 3 times to make a sphere. This can be used in general to make a sphere of radius R from a cube with an edge greater than R.

Since the volumes are equivalent (by design) and RHDO is nearly spherical, the sphere can be converted to RHDO by simply imposing the crystal lattice and minimizng. I then equilibrated with a few 100 ps of dynamics, before using it as a solvent bath for some simulations.

By using the volume formula for RHDO in crystl.doc and that for the volume of a sphere, you can establish the sphere radius needed for an RHDO with any value of A.


Edited by rmv (04/03/04 05:52 PM)
_________________________
Rick Venable
computational chemist


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#1186 - 04/04/04 02:59 PM Re: RHDO water box [Re: rmv]
dmr Offline
Forum Member

Registered: 04/02/04
Posts: 9
Loc: University of Wisconsin, Madis...
Thanks for the response!

-Demian

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