[gmx-users] Place water away from existing atoms

Justin A. Lemkul jalemkul at vt.edu
Thu May 17 15:06:05 CEST 2012

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.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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