On 10/3/12 8:59 AM, James Starlight wrote:
Justin,
Might the modifications of the vdwradii.dat be suitable for such
system expanding or (on other hand) reduction (as in the below picture
are shown). In the lattter case I defined new box dimensions (smaller
than initial box dims) and would like to remove all side water-lipids
layer which are beyond new pbc dimensions)?
http://imageshack.us/content_round.php?page=done&l=img138/5497/reduction.png
I don't know if that will have much of an effect or not. The values in
vdwradii.dat are used to determine if there is atomic overlap with coordinates
being added (solvent) to the solute configuration.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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