On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo <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? Steven > > El 17/05/12 12:25, Steven Neumann escribió: > > Dear Gmx users, > > My system consists of a tube which is representated by atoms which are not > connected via bonds. > genbox somehow place water molecules overlapping my tube atoms resulting > in bad contacts. > > Is there anyway to add water e.g. 4A away from existing index file of my > tube? > > Please, help. > > Steven > > > > -- > Javier CEREZO BASTIDA > PhD Student > Physical Chemistry > Universidad de Murcia > Murcia (Spain) > Tel: (+34)868887434 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 >
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