[gmx-users] Re: Steepest LINCS WARNING

Sat Jun 8 12:40:50 CEST 2013

Seems something http://www.gromacs.org/Documentation/Terminology/Blowing_Up,
probably because there is something nonsensical about your starting
configuration. Try to simplify things, visualize the configuration, don't
ignore warnings.

Mark

On Sat, Jun 8, 2013 at 7:10 AM, maggin <maggin.chen at gmail.com> wrote:

> when I first run enery minimization in vacuum, then add water model,
> (I use GROMOS96 53a6 force field, and  spce water model)
>
> EM in water model:
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+03
>    Number of steps    =         2000
> Step=    0, Dmax= 5.0e-03 nm, Epot= -3.51690e+05 Fmax= 2.16580e+04, atom=
> 21005
> Step=    1, Dmax= 5.0e-03 nm, Epot= -3.60975e+05 Fmax= 1.24353e+04, atom=
> 3050
> Step=    2, Dmax= 6.0e-03 nm, Epot= -3.73328e+05 Fmax= 8.74189e+03, atom=
> 3050
> Step=    3, Dmax= 7.2e-03 nm, Epot= -3.85332e+05 Fmax= 5.54552e+03, atom=
> 3050
> Step=    4, Dmax= 8.6e-03 nm, Epot= -3.98300e+05 Fmax= 3.03988e+03, atom=
> 20120
> Step=    5, Dmax= 1.0e-02 nm, Epot= -4.13757e+05 Fmax= 1.75853e+03, atom=
> 29072
> Step=    6, Dmax= 1.2e-02 nm, Epot= -4.29896e+05 Fmax= 1.55053e+03, atom=
> 29072
> Step=    7, Dmax= 1.5e-02 nm, Epot= -4.42239e+05 Fmax= 1.28428e+03, atom=
> 29072
> Step=    8, Dmax= 1.8e-02 nm, Epot= -4.53744e+05 Fmax= 1.40998e+03, atom=
> 920
> Step=    9, Dmax= 2.1e-02 nm, Epot= -4.61547e+05 Fmax= 4.89215e+03, atom=
> 520
> Step=   10, Dmax= 2.6e-02 nm, Epot= -4.63542e+05 Fmax= 5.75251e+03, atom=
> 516
> Step=   11, Dmax= 3.1e-02 nm, Epot= -4.64658e+05 Fmax= 5.56526e+03, atom=
> 520
>
> Step 12, time 0.024 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.004301, max 0.126066 (between atoms 512 and 516)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     512    516   39.0    0.1472   0.1565      0.1390
>     514    518   38.5    0.1467   0.1558      0.1390
>     516    520   38.8    0.1472   0.1557      0.1390
>     518    520   38.7    0.1471   0.1550      0.1390
>     511    514   39.7    0.1466   0.1561      0.1390
>     511    512   40.1    0.1470   0.1561      0.1390
> Step=   13, Dmax= 1.9e-02 nm, Epot= -4.67377e+05 Fmax= 3.11093e+03, atom=
> 5116
> Step=   15, Dmax= 1.1e-02 nm, Epot= -4.68747e+05 Fmax= 2.97283e+03, atom=
> 520
> Step=   16, Dmax= 1.3e-02 nm, Epot= -4.70028e+05 Fmax= 3.63802e+03, atom=
> 516
> Step=   17, Dmax= 1.6e-02 nm, Epot= -4.71166e+05 Fmax= 4.03533e+03, atom=
> 520
> Step=   18, Dmax= 1.9e-02 nm, Epot= -4.71943e+05 Fmax= 4.96009e+03, atom=
> 516
> Step=   19, Dmax= 2.3e-02 nm, Epot= -4.72558e+05 Fmax= 5.15705e+03, atom=
> 520
> Step=   21, Dmax= 1.4e-02 nm, Epot= -4.75111e+05 Fmax= 1.55977e+03, atom=
> 511
> Step=   22, Dmax= 1.7e-02 nm, Epot= -4.75363e+05 Fmax= 5.38247e+03, atom=
> 582
> Step=   23, Dmax= 2.0e-02 nm, Epot= -4.77689e+05 Fmax= 3.75868e+03, atom=
> 159
> Step=   25, Dmax= 1.2e-02 nm, Epot= -4.79001e+05 Fmax= 2.54107e+03, atom=
> 159
> Step=   26, Dmax= 1.4e-02 nm, Epot= -4.79210e+05 Fmax= 4.39836e+03, atom=
> 159
> Step=   27, Dmax= 1.7e-02 nm, Epot= -4.80268e+05 Fmax= 3.94950e+03, atom=
> 159
> Step=   29, Dmax= 1.0e-02 nm, Epot= -4.81704e+05 Fmax= 1.36796e+03, atom=
> 159
> Step=   30, Dmax= 1.2e-02 nm, Epot= -4.82183e+05 Fmax= 4.55734e+03, atom=
> 159
> Step=   31, Dmax= 1.5e-02 nm, Epot= -4.83601e+05 Fmax= 2.65995e+03, atom=
> 159
> Step=   33, Dmax= 8.9e-03 nm, Epot= -4.84347e+05 Fmax= 2.05512e+03, atom=
> 159
> Step=   34, Dmax= 1.1e-02 nm, Epot= -4.84811e+05 Fmax= 3.30097e+03, atom=
> 159
> Step=   35, Dmax= 1.3e-02 nm, Epot= -4.85461e+05 Fmax= 3.18540e+03, atom=
> 159
> Step=   36, Dmax= 1.5e-02 nm, Epot= -4.85605e+05 Fmax= 4.31161e+03, atom=
> 159
> Step=   37, Dmax= 1.9e-02 nm, Epot= -4.85983e+05 Fmax= 4.53453e+03, atom=
> 159
> Step=   39, Dmax= 1.1e-02 nm, Epot= -4.87596e+05 Fmax= 1.03948e+03, atom=
> 366
> Step=   40, Dmax= 1.3e-02 nm, Epot= -4.87792e+05 Fmax= 4.95272e+03, atom=
> 159
> Step=   41, Dmax= 1.6e-02 nm, Epot= -4.89343e+05 Fmax= 2.61653e+03, atom=
> 159
> Step=   43, Dmax= 9.6e-03 nm, Epot= -4.89881e+05 Fmax= 2.44528e+03, atom=
> 159
> Step=   44, Dmax= 1.2e-02 nm, Epot= -4.90124e+05 Fmax= 3.33456e+03, atom=
> 159
> Step=   45, Dmax= 1.4e-02 nm, Epot= -4.90496e+05 Fmax= 3.58399e+03, atom=
> 159
> Step=   47, Dmax= 8.3e-03 nm, Epot= -4.91468e+05 Fmax= 6.25094e+02, atom=
> 366
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up em_constrain.gro to ./#em_constrain.gro.2#
>
> Steepest Descents converged to Fmax < 1000 in 48 steps
> Potential Energy  = -4.9146806e+05
> Maximum force     =  6.2509442e+02 on atom 366
> Norm of force     =  6.6710007e+01
>
> LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.004301, max 0.126066 (between atoms 512 and 516)
> ATOM    512  HD2 ARG A 156     -13.495  -6.447  -3.087  1.00  0.00
> H
> ATOM    516  NH1 ARG A 156     -14.923  -9.012  -5.069  1.00  0.00
> N
>
> Befor EM in vacuum, there are 4 LINCS WARNING; now there are only one,
> But I have no idea what can I do, to kill this LINCS WARNING?
> Thank you very much!
> maggin
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Steepest-LINCS-WARNING-tp5008919p5008920.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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