On Mon, Apr 1, 2013 at 7:55 AM, Zhikun Cai <caiz...@gmail.com> wrote:
> Hi all, > > I would like to add 484 water molecules into the box using command: > > genbox -cp newbox.gro -cs tip4p.gro -maxsol 484 -p topol.top -o > solvated.gro > > > What I expected is those water molecules would be randomly inserted into > the box and the box should appear homogeneous. But the result disappointed > me. Throught VMD, I found that the 484 water molecues was inserted almost > in one half of the box. Then when I added more water molecules, they began > to occupy the other half box. > > So what could I do to make the inserted 484 water molecules randomly > positioned in the box in the beginning? > Your advice would be highly appreciated. > > The -cs solvation mechanism adds solvent in a grid-based approach, so the outcome you report is exactly what is expected. If you want random insertion of a certain number of solvent molecules, then you should use the -ci -nmol option, providing the coordinate file of a single water molecule to the -ci flag. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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
