On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/18/13 2:56 PM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I am trying to obtain given density for my system for a given molecule >> - its a cubic box of 5 nm in dimension. >> >> I calculated that I need 850 molecules to get the density of 500 g/mol >> In my box there is already 1 molecule so I try: >> >> genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb >> >> >> >> Added 819 molecules (out of 849 requested) >> Output configuration contains 9020 atoms in 820 residues >> Volume : 125 (nm^3) >> Density : 480.336 (g/l) >> Number of SOL molecules: 0 >> >> How can I add 30 more molecules using gromacs? I want to avoid adding >> it manually. >> > > Use a larger box and equilibrate.
Thanks. Larger box will need more molecules which is quite obvious so the same problem occurs. I need a cubic box first with given fixed density and then equilibrate it. Further step is to extend the box in one dimension to get properties I want. Shall manually add them then? Steven All genbox tries to do is add molecules > randomly, which is not a foolproof process. If the force field parameters > indeed produce the correct density, you should be able to produce it rather > quickly. > > -Justin > > -- > ======================================== > > 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 > > ======================================== > -- > 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 -- 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