Hi Justin Thank you for your suggestion.
Regards Vinoth On Mon, Sep 27, 2010 at 4:52 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi justin >> >> if genbox is not able to find sufficient space then why should one >> calculate number density for the given box dimension?.similarly the the >> > > Just because you can calculate a certain number density does not > necessarily mean that the algorithm genbox is using can produce such a > configuration. It inserts molecules randomly, so you may be able to find a > magical value of -seed for which this will work. The simpler approach is > what I suggested earlier. > > number of molecules are not getting updated in the molecules section of >> the topology file when inserting multiple molecules using the genbox >> command. everytime i need to update it manually.is <http://manually.is> >> there a way to update it automatically? >> >> > The topology will only be updated automatically when adding water. > Otherwise, you have to do it yourself. > > -Justin > > Regards >> Vinoth >> >> >> On Mon, Sep 27, 2010 at 4:31 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> vinothkumar mohanakrishnan wrote: >> >> Hi all >> >> I have a diffculty in adding multiple molecules of hexane to my >> box. my box size is 4.72*2.36*2.36 (nm) according to my number >> density calculations the box should fit 124 molecules of hexane >> whereas it adds only 76 molecules to the box below is my >> command. i had evev tried with -try command but without sucess. >> >> genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o >> hexane-multi.gro -nmol 124 -seed 1268 >> >> >> If you're not getting all the molecules you want, then genbox is >> unable to find sufficient space for them. Try a larger box, then >> equilibrate. >> >> -Justin >> >> Regards >> Vinoth >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > 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 > 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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