[gmx-users] Place water away from existing atoms

[Justin A. Lemkul]

On 5/17/12 9:00 AM, Steven Neumann wrote:
>
>
> On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo <jcb1 at um.es <mailto:jcb1 at 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

-- 
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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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