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?
Sincerely, Shima ________________________________ From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Friday, April 5, 2013 7:42 PM Subject: Re: Fw: [gmx-users] water molecule can not be settled On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh <shima_arasteh2...@yahoo.com> wrote: I' d like to know if it is acceptable to change the molecule coordinates to solve this problem? > > It's unlikely that some ad hoc change will magically fix a problem. Energy minimization should take care of clashes. Some time back, I deleted such a molecule and then I got a fatal error containing that the trj file and other inputs are not inconsistent. > > Right, because you've now changed the contents of the system. It no longer matches the topology and the trajectory would then be discontinuous. -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 * 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
