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