[gmx-users] Place water away from existing atoms

[Steven Neumann]

On Thu, May 17, 2012 at 2:06 PM, Justin A. Lemkul <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>>
>>
>> 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?

Steven


> --
> ==============================**==========
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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
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