If you use v-rescale their is a very small probability that this is caused by a fixed error in GROMACS.
On Fri, Oct 22, 2010 at 6:23 PM, Justin A. Lemkul <[email protected]> wrote: > > > Xu Danial wrote: > >> Hi, >> >> >> My system was well equilibrated, but still crashed within 1ns simulation >> due to the following information: >> >> >> Fatal error: >> 28 particles communicated to PME node 48 are more than 2/3 times the >> cut-off out of >> the domain decomposition cell of their charge group in dimension y. >> >> >> I wonder is this problem already solved in GMX4.5.1 ? >> >> > I doubt this is a problem that needs to be fixed within Gromacs. In all > likelihood, your system is unstable: > > > http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group > > Unless you have specific evidence demonstrating that Gromacs crashed > inappropriately, the problem lies with your system. Likely it is not as > well equilibrated as you believe. > > -Justin > > >> >> Thanks >> >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
