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
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