On 5/17/12 9:00 AM, Steven Neumann wrote:
On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo <j...@um.es <mailto:j...@um.es>>
wrote:
genbox calculates overlaps based on vdW radii as included in vdwradii.dat in
the topology folder. Increase the vdW radii of carbons to avoid water to
closer that you want. Other possibilities are patiently removing undesired
waters by hand after solvation or using a "ad-hoc" script.
Javier
Thank you Javier. Can you please explain what is ad-hoc script and where I can
find it?
The term "ad hoc" simply means something designed for a specific task, i.e. a
script you would write yourself.
The logic behind such a script is discussed in the following wiki page, though
it is designed for membrane solvation and you would have to amend it
considerably to suit your purpose.
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations
-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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