On 5/17/12 9:24 AM, Steven Neumann wrote:
On Thu, May 17, 2012 at 2:06 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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> <mailto: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
<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
--
========================================
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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