Thanks so much for your replies. I appreciate you. Do you think that more NPT equilibration might solve the problem? or wont work?
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, April 19, 2013 11:23 PM Subject: Re: [gmx-users] unstable system On 4/19/13 2:49 PM, Shima Arasteh wrote: > The energy minimization has been done and the result is as follow: > > Steepest Descents converged to Fmax < 100 in 8971 steps > Potential Energy = -1.5253394e+06 > Maximum force = 9.2729095e+01 on atom 4719 > Norm of force = 3.5977371e+00 > > But by running mdrun, I get this fatal error: > 1 particles communicated to PME node 4 are more than 2/3 times the cut-off > out of the domain decomposition cell of their charge group in dimension x. > > > So needs more npt? > I have no idea what this means. The minimization looks perfect. Continue with whatever equilibration scheme you think is appropriate. -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 -- 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
