[gmx-users] Place water away from existing atoms

[Steven Neumann]

On Thu, May 17, 2012 at 2:30 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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>
>>
>>    <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


Thank you Justin. In my case each atoms is a representation of a residue. I
do not want to have any water inside of my tube as well. Now as less atoms
are inside I can easier remove them manually.

Steven


>
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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