[gmx-users] minimization problem

[Itamar Kass]

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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>
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