On Fri, Apr 5, 2013 at 3:05 PM, Albert <mailmd2...@gmail.com> wrote: > Hello: > > I found that there would be some problem of genion in 4.6.1: > > grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr > > NOTE 1 [file complex.top, line 44008]: > System has non-zero total charge: -11.000000 > Total charge should normally be an integer. See > > http://www.gromacs.org/**Documentation/Floating_Point_**Arithmetic<http://www.gromacs.org/Documentation/Floating_Point_Arithmetic> > for discussion on how close it should be to an integer. > > > genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom > > Reading file ions.tpr, VERSION 4.6.1 (single precision) > Using a coulomb cut-off of 1.2 nm > No ions to add and no potential to calculate. > > Obviously, the total charge of the system is -11.0, but genion doesn't add > anything to netural it.... > > > genion has never done anything if you just use -neutral. You need to use -neutral in conjunction with -conc, otherwise manually specify the number of ions to add.
-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
