On Thu, May 17, 2012 at 2:30 PM, Justin A. Lemkul <jalem...@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 <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> >> >> >> <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> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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