[gmx-users] error in mdrun

[reisingere at rostlab.informatik.tu-muenchen.de]

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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