[gmx-users] minimization problem

[Mark Abraham]

Paymon Pirzadeh wrote:
> Hello,
> I merged two simulation boxes, 

Are you sure your error is not here? Inspect your result visually! :-) 
All the atoms need to be inside the box and non-overlapping.

Mark

> 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
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>