[gmx-users] Place water away from existing atoms

[Justin A. Lemkul]

On 5/17/12 9:24 AM, Steven Neumann wrote:
>
>
> On Thu, May 17, 2012 at 2:06 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     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> <mailto: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
>     <http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations>
>
>     -Justin
>
>
>
> Thank you. Ok, I added the residues and atoms to vdwradii.dat with higher vdw
> radius as I created my own atoms belonging to the tube. Without vdwradii.dat
> containing atoms of my tube 10 000 water molecules were added (denity app 1000
> g/L). Using the vdwradii.dat app 6000 water molecules were added decreasing
> density of water obviosuly.
> My question: Are distances between water molecules will be affected or just
> between my Tube atoms (specified in vdwradii.dat) and water molecules as the
> number of water molecules decreased rapidly?
>

Changes to vdwradii.dat make the atoms seem larger, so that genbox detects a 
clash when it tries to add a water molecule near the "larger" atoms.  The end 
result is a void around the "larger" atoms such that your density decreases. 
This strategy simply makes it less likely that there will be a water molecule 
near a tube atom.  It may become impractical to continually increase the 
radius/radii of your tube atom type(s) in such a way that it will completely 
eliminate the addition of water inside, in which case scripting or manual 
deletion is necessary.

-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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