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?<br>
<br><div class="gmail_quote">Steven<br><br>On Thu, May 17, 2012 at 2:44 PM, Steven Neumann <span dir="ltr"><<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br><br><div class="gmail_quote"><div><div class="h5">On Thu, May 17, 2012 at 2:30 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><br>
<br>
On 5/17/12 9:24 AM, Steven Neumann wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
<br>
<br>
On Thu, May 17, 2012 at 2:06 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div><div>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
On 5/17/12 9:00 AM, Steven Neumann wrote:<br>
<br>
<br>
<br>
On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo <<a href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a><br></div>
<mailto:<a href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a>> <mailto:<a href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a> <mailto:<a href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a>>>><div>
<br>
<br>
wrote:<br>
<br>
genbox calculates overlaps based on vdW radii as included in<br>
vdwradii.dat in<br>
the topology folder. Increase the vdW radii of carbons to avoid water to<br>
closer that you want. Other possibilities are patiently removing<br>
undesired<br>
waters by hand after solvation or using a "ad-hoc" script.<br>
<br>
Javier<br>
<br>
<br>
Thank you Javier. Can you please explain what is ad-hoc script and where<br>
I can<br>
find it?<br>
<br>
<br>
The term "ad hoc" simply means something designed for a specific task, i.e.<br>
a script you would write yourself.<br>
<br>
The logic behind such a script is discussed in the following wiki page,<br>
though it is designed for membrane solvation and you would have to amend it<br>
considerably to suit your purpose.<br>
<br></div>
<a href="http://www.gromacs.org/__Documentation/How-tos/__Membrane_Simulations" target="_blank">http://www.gromacs.org/__<u></u>Documentation/How-tos/__<u></u>Membrane_Simulations</a><div><br>
<<a href="http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/<u></u>Membrane_Simulations</a>><br>
<br>
-Justin<br>
<br>
<br>
<br>
Thank you. Ok, I added the residues and atoms to vdwradii.dat with higher vdw<br>
radius as I created my own atoms belonging to the tube. Without vdwradii.dat<br>
containing atoms of my tube 10 000 water molecules were added (denity app 1000<br>
g/L). Using the vdwradii.dat app 6000 water molecules were added decreasing<br>
density of water obviosuly.<br>
My question: Are distances between water molecules will be affected or just<br>
between my Tube atoms (specified in vdwradii.dat) and water molecules as the<br>
number of water molecules decreased rapidly?<br>
<br>
</div></blockquote>
<br>
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.<span><font color="#888888"><br>
<br>
-Justin</font></span></blockquote></div></div><div><br>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.<span class="HOEnZb"><font color="#888888"><br>
<br>Steven<br> </font></span></div><div class="im"><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
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