[gmx-users] minimization problem

[Itamar Kass]

I am not sure what you refer to as dt, as there no meaning to time in  
EM.

Anyway, I think the easiest way is to remove this ware molecule.

Best,
Itamar.

On 26/10/2009, at 10:31 AM, 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?
> Regards,
>
> Payman
>
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