You mean start over the NPT step?
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, April 5, 2013 7:50 PM Subject: Re: Fw: [gmx-users] water molecule can not be settled On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh <shima_arasteh2...@yahoo.com>wrote: > As I visualized the system, I see a water molecule somewhere between lipid > chains near the protein entrance. This has been happen during NPT. I' d > like to delete this molecule but with such a kind of fatal error this would > impossible. So what's the way? Is there any tricky way to change > coordinate of molecule? but I seems also impossible becasue PME problem! > So whats the solution? > > Delete the molecule, adjust your topology (and index file, if necessary), and start over with the equilibration. -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 -- 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