Justin, Simeone will insert only "the needed number of waters" but not the full box. :) To do so he will use an option "-maxsol XXX" of genbox.
Vitaly On Mon, Sep 28, 2009 at 5:08 PM, Justin A. Lemkul <[email protected]> wrote: > > > Vitaly V. Chaban wrote: >> >> Hi Simone, >> >> I would advise you to insert the needed number of waters (genbox -cp >> conf.gro -cs water.gro -o conf1.gro) and then do the same with DMSO >> ((genbox -cp conf1.gro -cs dmso.gro -o conf2.gro). Then just >> equilibrate. >> > > I doubt that will work. The first call to genbox there will fill the box > with water, leaving no room for anything else. > > -Justin > >> Vitaly >> >> >>> I need to run a simulation of a protein in a water/DMSO mixture. I can't >>> quite understand how should I do this... should I normally solvate the >>> protein with water and then replace a certain number of water molecules >>> (according to the needed % of DMSO) with DMSO molecules? But in this >>> case, >>> how should I do it? Is there a way of replacing solvent molecules with >>> other >>> solvent molecules, but of a different type? >>> I'm sorry but I don't know which procedure to follow. >>> Thanks in advance _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
