[gmx-users] error in mdrun

Mon Jul 9 15:46:19 CEST 2012

With the mentioned below options I get the following error:

Fatal error:
1 particles communicated to PME node 1 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

But it does not occur immediatly but only at step

Step 695, time 1.39 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.011725, max 78.611298 (between atoms 3778 and 3781)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3782   3785   92.2    1.3061   0.2785      0.1090
   3782   3784   93.0    0.1055   0.2552      0.1090
   3782   3783   91.0    0.1062   0.3086      0.1090
   3204   3206   89.6    0.1449   1.0256      0.1449
   3204   3205   89.7    0.1010   0.9949      0.1010

Is there something wrong with my temperature coupling?

Thank you,
Eva

> Hi Justin,
>  okey then I will try it with this timestep.
> No it is not my goal to do a NVE. I already had temperature coupling
> options in my .mdp file but on the blowing up side was written "you are
> using inappropriate temperature coupling" so I thought that that might be
> the reason and deleted it from my .mdp file.
>
> I had the following temperature coupling options:
>
> tcoupl          = V-rescale
> tc-grps         = Protein  Non-Protein
> tau_t           = 0.1      0.1
> ref_t           = 298      298
> pcoupl          = no
>
>
>
> Thank you for your answer.
> Eva
>
>>
>>
>> On 7/9/12 9:25 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>>> Hi everybody,
>>> I want to do a md for a protein with a membrane around it.
>>> I already minimised the energy of the protein.
>>>
>>>
>>>
>>> Output of the minimization:
>>>
>>> ^MStep=  812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02,
>>> atom= 1653
>>> Stepsize too small, or no change in energy.
>>> Converged to machine precision,
>>> but not to the requested precision Fmax < 10
>>>
>>> Double precision normally gives you higher accuracy.
>>> You might need to increase your constraint accuracy, or turn
>>> off constraints alltogether (set constraints = none in mdp file)
>>>
>>> writing lowest energy coordinates.
>>>
>>>
>>> Steepest Descents converged to machine precision in 813 steps,
>>> but did not reach the requested Fmax < 10.
>>> Potential Energy  = -7.5928356e+05
>>> Maximum force     =  3.6197971e+02 on atom 1653
>>> Norm of force     =  2.6517429e+00
>>>
>>>
>>>
>>>
>>>
>>> In my eyes this output was okey so I went on with the md.
>>> And here I get the error:
>>>
>>> Fatal error:
>>> A charge group moved too far between two domain decomposition steps
>>> This usually means that your system is not well equilibrated
>>>
>>>
>>>
>>>
>>> I already read the error page for this error and also the blowing up
>>> page
>>> but I still do not know what to do now.
>>>
>>> My .mdp file for the md runs looks like this:
>>>
>>> define          = -DPOSRES
>>> integrator              = md
>>> dt                      = 0.005
>>
>> This timestep is huge.  Even with constraints, you probably can't exceed
>> 2
>> fs
>> stably (0.002 ps).
>>
>>> nsteps          = 2000
>>> nstxout         = 0
>>> nstvout         = 0
>>> nstfout         = 0
>>> nstlog          = 1000
>>> nstxtcout               = 0
>>> nstenergy               = 5
>>> energygrps              = Protein Non-Protein
>>> nstcalcenergy   = 5
>>> nstlist         = 10
>>> ns-type         = Grid
>>> pbc                     = xyz
>>> rlist           = 0.9
>>> coulombtype             = PME
>>> rcoulomb                = 0.9
>>> rvdw            = 0.9
>>> fourierspacing          = 0.12
>>> pme_order               = 4
>>> ewald_rtol              = 1e-5
>>> gen_vel         = yes
>>> gen_temp                = 200.0
>>> gen_seed                = 9999
>>> constraints             = all-bonds
>>>
>>>
>>> Are here any optinos which can cause the error?
>>>
>>
>> In the absence of temperature and/or pressure coupling, the ensemble
>> you're
>> trying to simulate is NVE, which is very tricky to get stabilized.
>>
>> http://www.gromacs.org/Documentation/Terminology/NVE
>>
>> If you're not going for an NVE ensemble, you need several adjustments in
>> the
>> .mdp file.  See any basic tutorial for examples of how to simulate other
>> ensembles, if this is your goal.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> 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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