[gmx-users] error in mdrun

[Justin A. Lemkul]

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

-- 
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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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