I think it is too small. Try removing the water molecule and repeat
the EM. You might need to remove some molecules before you can
minimise your system.
Itamar
On 26/10/2009, at 10:48 AM, Paymon Pirzadeh wrote:
Sorry,
That was a big typo(a mis-pasted line)!!!!!
What is the suggestion anyway about emstep?
Payman
On Mon, 2009-10-26 at 10:43 +1100, Itamar Kass wrote:
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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