[gmx-users] Place water away from existing atoms
Justin A. Lemkul
jalemkul at vt.edu
Thu May 17 15:30:01 CEST 2012
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>>>
> 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
> waters by hand after solvation or using a "ad-hoc" script.
> 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.
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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