Thanks Justin, But I want to neutralize my system in implicit solvent. In Amber I had use Debye screening but in gromacs I don't know what should I do.
On Wed, Jul 11, 2012 at 2:45 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > On 7/11/12 6:00 AM, amir abbasi wrote: >> >> Hi All! >> I want to use Implicit solvent to simulate a nucleic acid sequence. >> How can I do it? >> I use this command: >> genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname >> CL -neutral -conc 0.1 >> >> ions.tpr file is same as umbrella sampling tutorial. >> >> I got this error message: >> Fatal error: >> Your solvent group size (2898) is not a multiple of 31 >> what should I do? >> > > One does not typically add explicit ions in an implicit solvent system. > genion fails because it appears you are trying to replace parts of your > nucleic acid with ions. > > -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 > * Only plain text messages are allowed! > * 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 * Only plain text messages are allowed! * 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