Joanne Martin wrote:
Hi im trying to run an NVT equilibration, and im getting the following
errors
these are my commands for solvating the box...........
any suggestions would be greatly appreciated
J
Did you search the Gromacs website and/or mailing list archive?
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
-Justin
editconf -f 2VVSET_complex.gro -o 2VVSET_complex_conf.gro -box 12
genbox -cp 2VVSET_complex_conf.gro -cs
/programs/gromacs-4.0.4/share/gromacs/top/ffamber_tip3p -o
2VVSET_complex_SOL.gro -p 2VVS_complex.top
output
starting mdrun 'Protein in water'
200000 steps, 400.0 ps.
Warning: 1-4 interaction between 4346 and 4350 at distance 3.066 which
is larger than the 1-4 table size 1.900 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
MPI Application rank 19 killed before MPI_Finalize() with signal 11
MPI Application rank 17 killed before MPI_Finalize() with signal 11
-------------------------------------------------------
Program mdrun_mpi4.0.4, VERSION 4.0.4
Source code file: pme.c, line: 518
Fatal error:
3 particles communicated to PME node 7 are more than a cell length out
of the domain decomposition cell of their charge group
--
========================================
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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