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
========================================
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