[gmx-users] Place water away from existing atoms

[Steven Neumann]

Well, I am still getting the same error when I try to do minimization:
"water molecule on atom X cannot be settled" - these water molecules are
not close to the Tube surface. If I will remove them the same error will
occur but on the other atoms. If I specified only vdwradii for my Tube
atoms why in the bulk of water there are some overlaps? Can you please help?

Steven

On Thu, May 17, 2012 at 2:44 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

>
>
> 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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>
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