Paymon Pirzadeh wrote:
Hello,
I merged two simulation boxes, and now I want to perform a minimization
to remove the problems at their boundary! I have reduced the dt to
0.000000001 and emstep to 0.000000001 as well. But still I get the
message
Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double precision)
Making 1D domain decomposition 8 x 1 x 1
Steepest Descents:
Tolerance (Fmax) = 1.00000e-05
Number of steps = 705032704
t = 0.000 ps: Water molecule starting at atom 190501 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
-------------------------------------------------------
Program mdrun_d_mpi, VERSION 4.0.5
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
as part of my error message. Should I still reduce the mentioned
parameters?
Please see here:
http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain.0adecomposition_cell_of_their_charge_group
If energy minimization is failing at step 0, there is probably some unresolvable
geometry that is stopping the process. Evaluate how you built the system, and
see what might be causing large forces.
-Justin
Regards,
Payman
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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