[gmx-users] Re: minimization problem

[Justin A. Lemkul]

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
> 
> 

-- 
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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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