GROMACS version:
GROMACS modification: Yes/No
Please suggest do i need to take any action or i can ignore and go ahed with below step 13: One or more water molecules can not be settled. and step 28: One or more water molecules can not be settled?:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= 6.60209e+07 Fmax= 1.60721e+10, atom= 17222
Step= 1, Dmax= 1.0e-02 nm, Epot= -2.03359e+06 Fmax= 2.30368e+08, atom= 17222
Step= 2, Dmax= 1.2e-02 nm, Epot= -3.35475e+06 Fmax= 5.27653e+06, atom= 17222
Step= 3, Dmax= 1.4e-02 nm, Epot= -3.43058e+06 Fmax= 1.36737e+06, atom= 17207
Step= 4, Dmax= 1.7e-02 nm, Epot= -3.54372e+06 Fmax= 3.52260e+05, atom= 17223
Step= 5, Dmax= 2.1e-02 nm, Epot= -3.81030e+06 Fmax= 8.36361e+04, atom= 17261
Step= 6, Dmax= 2.5e-02 nm, Epot= -4.19820e+06 Fmax= 2.30693e+04, atom= 9949
Step= 7, Dmax= 3.0e-02 nm, Epot= -4.50048e+06 Fmax= 3.03997e+04, atom= 17255
Step= 8, Dmax= 3.6e-02 nm, Epot= -4.58450e+06 Fmax= 3.24510e+04, atom= 17255
Step= 9, Dmax= 4.3e-02 nm, Epot= -4.64982e+06 Fmax= 1.59175e+04, atom= 17255
Step= 10, Dmax= 5.2e-02 nm, Epot= -4.76073e+06 Fmax= 5.54114e+04, atom= 17255
Step= 11, Dmax= 6.2e-02 nm, Epot= -4.78947e+06 Fmax= 1.37796e+04, atom= 17255
Step= 12, Dmax= 7.4e-02 nm, Epot= -4.88564e+06 Fmax= 1.00211e+05, atom= 9205
step 13: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step= 14, Dmax= 4.5e-02 nm, Epot= -4.90195e+06 Fmax= 3.53101e+04, atom= 92055
Step= 15, Dmax= 5.3e-02 nm, Epot= -4.92461e+06 Fmax= 3.60905e+04, atom= 9205
Step= 16, Dmax= 6.4e-02 nm, Epot= -4.94646e+06 Fmax= 4.94189e+04, atom= 9205
Step= 17, Dmax= 7.7e-02 nm, Epot= -4.96493e+06 Fmax= 5.51652e+04, atom= 9205
Step= 18, Dmax= 9.2e-02 nm, Epot= -4.98156e+06 Fmax= 6.76785e+04, atom= 9205
Step= 19, Dmax= 1.1e-01 nm, Epot= -4.99492e+06 Fmax= 1.24357e+05, atom= 9205
Step= 20, Dmax= 1.3e-01 nm, Epot= -5.01060e+06 Fmax= 8.10146e+04, atom= 9205
Step= 21, Dmax= 1.6e-01 nm, Epot= -5.02085e+06 Fmax= 1.26050e+05, atom= 9205
Step= 22, Dmax= 1.9e-01 nm, Epot= -5.03966e+06 Fmax= 5.55995e+04, atom= 9205
Step= 25, Dmax= 5.8e-02 nm, Epot= -5.05587e+06 Fmax= 5.70279e+04, atom= 9205
Step= 26, Dmax= 6.9e-02 nm, Epot= -5.06603e+06 Fmax= 4.24640e+04, atom= 9205
Step= 27, Dmax= 8.3e-02 nm, Epot= -5.07767e+06 Fmax= 1.63888e+05, atom= 9205
step 28: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step= 29, Dmax= 5.0e-02 nm, Epot= -5.08515e+06 Fmax= 2.81433e+04, atom= 9205
Step= 30, Dmax= 6.0e-02 nm, Epot= -5.10068e+06 Fmax= 3.79215e+04, atom= 9205
Step= 31, Dmax= 7.2e-02 nm, Epot= -5.11230e+06 Fmax= 6.56359e+04, atom= 9205
Step= 32, Dmax= 8.6e-02 nm, Epot= -5.12237e+06 Fmax= 5.25851e+04, atom= 9205
Step= 33, Dmax= 1.0e-01 nm, Epot= -5.13104e+06 Fmax= 1.10335e+05, atom= 9205
Step= 34, Dmax= 1.2e-01 nm, Epot= -5.14161e+06 Fmax= 4.20119e+04, atom= 9205 …
Step= 832, Dmax= 1.1e-02 nm, Epot= -5.81777e+06 Fmax= 7.76055e+03, atom= 9284
Step= 833, Dmax= 1.3e-02 nm, Epot= -5.81778e+06 Fmax= 9.63210e+03, atom= 9284
Step= 835, Dmax= 7.6e-03 nm, Epot= -5.81830e+06 Fmax= 8.40019e+02, atom= 9303
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 1000 in 836 steps
Potential Energy = -5.8182965e+06
Maximum force = 8.4001923e+02 on atom 9303
Norm of force = 1.7506589e+01
Also if i edit my em.mdp with “define= -DFLEXIBLE” what will be the impact and is it rite to do that?
em.mdp (1.1 KB)
please suggest. Thanks