[gmx-users] minimization_error
Justin Lemkul
jalemkul at vt.edu
Sun Sep 9 21:02:34 CEST 2018
On 9/9/18 3:01 PM, Bratin Kumar Das wrote:
> Respected Dr justin,
> During minimisation I restrained all the
> heavy atom to 1000 and .mdp file I defined =-DPOSRES. But during
> minimization at 36th sept the following lines are coming
> step 36: One or more water molecules can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Back Off! I just backed up step36b.pdb to ./#step36b.pdb.1#
>
> Back Off! I just backed up step36c.pdb to ./#step36c.pdb.1#
> Can it creat any problem during equilibration?
Unlikely. As long as minimization completes normally (which it did), you
can safely disregard the mild bad contact. If minimization aborts after
such messages and/or huge forces remain, you will have a problem.
-Justin
> On Mon, Sep 10, 2018 at 12:24 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 9/9/18 2:53 PM, Bratin Kumar Das wrote:
>>
>>> Dear all,
>>> During minimization of a protein molecule I found following
>>> error
>>> Steepest Descents:
>>> Tolerance (Fmax) = 1.00000e+03
>>> Number of steps = 50000
>>> Step= 0, Dmax= 1.0e-02 nm, Epot= 7.31298e+11 Fmax= 2.45648e+14, atom=
>>> 4054
>>> Step= 1, Dmax= 1.0e-02 nm, Epot= 1.50885e+10 Fmax= 1.54878e+12, atom=
>>> 2379
>>> Step= 2, Dmax= 1.2e-02 nm, Epot= 1.64698e+09 Fmax= 8.54330e+10, atom=
>>> 2383
>>> Step= 3, Dmax= 1.4e-02 nm, Epot= 3.28739e+08 Fmax= 1.05704e+10, atom=
>>> 4048
>>> Step= 4, Dmax= 1.7e-02 nm, Epot= 8.36090e+07 Fmax= 1.51995e+09, atom=
>>> 4050
>>> Step= 5, Dmax= 2.1e-02 nm, Epot= 1.71898e+07 Fmax= 2.07116e+08, atom=
>>> 2389
>>> Step= 6, Dmax= 2.5e-02 nm, Epot= 2.12858e+06 Fmax= 3.24305e+07, atom=
>>> 2429
>>> Step= 7, Dmax= 3.0e-02 nm, Epot= -5.70125e+05 Fmax= 3.58609e+06, atom=
>>> 4049
>>> Step= 8, Dmax= 3.6e-02 nm, Epot= -1.28016e+06 Fmax= 1.65686e+06, atom=
>>> 4049
>>> Step= 9, Dmax= 4.3e-02 nm, Epot= -1.42968e+06 Fmax= 1.01298e+06, atom=
>>> 5961
>>> Step= 10, Dmax= 5.2e-02 nm, Epot= -1.49528e+06 Fmax= 6.36454e+06, atom=
>>> 5961
>>> Step= 11, Dmax= 6.2e-02 nm, Epot= -1.54938e+06 Fmax= 6.68748e+05, atom=
>>> 5961
>>> Step= 12, Dmax= 7.4e-02 nm, Epot= -1.65446e+06 Fmax= 1.20563e+06, atom=
>>> 5961
>>> Step= 13, Dmax= 8.9e-02 nm, Epot= -1.69075e+06 Fmax= 7.88571e+05, atom=
>>> 5961
>>> Step= 14, Dmax= 1.1e-01 nm, Epot= -1.75037e+06 Fmax= 3.41886e+05, atom=
>>> 5959
>>> Step= 15, Dmax= 1.3e-01 nm, Epot= -1.82276e+06 Fmax= 2.53773e+06, atom=
>>> 6040
>>> Step= 16, Dmax= 1.5e-01 nm, Epot= -1.84616e+06 Fmax= 7.83228e+04, atom=
>>> 6038
>>> Step= 17, Dmax= 1.8e-01 nm, Epot= -1.92394e+06 Fmax= 5.93584e+06, atom=
>>> 5959
>>> Step= 18, Dmax= 2.2e-01 nm, Epot= -1.95719e+06 Fmax= 1.40285e+06, atom=
>>> 5959
>>> Step= 22, Dmax= 3.3e-02 nm, Epot= -1.97156e+06 Fmax= 3.57269e+05, atom=
>>> 6035
>>> Step= 23, Dmax= 4.0e-02 nm, Epot= -1.98878e+06 Fmax= 1.96496e+05, atom=
>>> 6038
>>> Step= 24, Dmax= 4.8e-02 nm, Epot= -2.00989e+06 Fmax= 1.38405e+05, atom=
>>> 6038
>>> Step= 25, Dmax= 5.8e-02 nm, Epot= -2.03060e+06 Fmax= 7.56408e+04, atom=
>>> 6038
>>> Step= 26, Dmax= 6.9e-02 nm, Epot= -2.05304e+06 Fmax= 1.84679e+05, atom=
>>> 6035
>>> Step= 27, Dmax= 8.3e-02 nm, Epot= -2.06081e+06 Fmax= 1.93408e+05, atom=
>>> 6035
>>> Step= 28, Dmax= 9.9e-02 nm, Epot= -2.06913e+06 Fmax= 7.41533e+04, atom=
>>> 6035
>>> Step= 29, Dmax= 1.2e-01 nm, Epot= -2.09293e+06 Fmax= 2.36608e+05, atom=
>>> 6035
>>> Step= 30, Dmax= 1.4e-01 nm, Epot= -2.09915e+06 Fmax= 7.16045e+04, atom=
>>> 5956
>>> Step= 32, Dmax= 8.6e-02 nm, Epot= -2.12024e+06 Fmax= 1.92532e+04, atom=
>>> 6034
>>> Step= 33, Dmax= 1.0e-01 nm, Epot= -2.16233e+06 Fmax= 2.15331e+05, atom=
>>> 6034
>>> Step= 34, Dmax= 1.2e-01 nm, Epot= -2.16784e+06 Fmax= 2.29221e+05, atom=
>>> 6034
>>> Step= 35, Dmax= 1.5e-01 nm, Epot= -2.17775e+06 Fmax= 3.69837e+04, atom=
>>> 5954
>>>
>>> step 36: 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= 37, Dmax= 8.9e-02 nm, Epot= -2.19131e+06 Fmax= 6.98159e+04, atom=
>>> 5930
>>> Step= 38, Dmax= 1.1e-01 nm, Epot= -2.20081e+06 Fmax= 6.51073e+04, atom=
>>> 5930
>>> Step= 39, Dmax= 1.3e-01 nm, Epot= -2.20771e+06 Fmax= 5.28709e+04, atom=
>>> 5930
>>> Step= 41, Dmax= 7.7e-02 nm, Epot= -2.21916e+06 Fmax= 4.40351e+04, atom=
>>> 6034
>>> Step= 42, Dmax= 9.2e-02 nm, Epot= -2.22219e+06 Fmax= 8.88734e+04, atom=
>>> 6034
>>> Step= 43, Dmax= 1.1e-01 nm, Epot= -2.23435e+06 Fmax= 4.54206e+04, atom=
>>> 6038
>>> Step= 45, Dmax= 6.6e-02 nm, Epot= -2.24405e+06 Fmax= 2.58491e+04, atom=
>>> 6038
>>> Here you can see "step 36" why this warning is coming. To overcome that
>>> what can be done ...please comment
>>> after 2000 steps energy minimisation stopped..
>>> Step= 1990, Dmax= 1.2e-02 nm, Epot= -2.65978e+06 Fmax= 1.04066e+04, atom=
>>> 7047
>>> Step= 1991, Dmax= 1.5e-02 nm, Epot= -2.65979e+06 Fmax= 1.20911e+04, atom=
>>> 7047
>>> Step= 1993, Dmax= 8.7e-03 nm, Epot= -2.65989e+06 Fmax= 1.40821e+03, atom=
>>> 7047
>>> Step= 1994, Dmax= 1.0e-02 nm, Epot= -2.65990e+06 Fmax= 1.47325e+04, atom=
>>> 7047
>>> Step= 1995, Dmax= 1.3e-02 nm, Epot= -2.66002e+06 Fmax= 4.74074e+03, atom=
>>> 7047
>>> Step= 1997, Dmax= 7.5e-03 nm, Epot= -2.66004e+06 Fmax= 6.93813e+03, atom=
>>> 7047
>>> Step= 1998, Dmax= 9.1e-03 nm, Epot= -2.66006e+06 Fmax= 7.07361e+03, atom=
>>> 7047
>>> Step= 2000, Dmax= 5.4e-03 nm, Epot= -2.66010e+06 Fmax= 1.33089e+03, atom=
>>> 7047
>>> Step= 2001, Dmax= 6.5e-03 nm, Epot= -2.66013e+06 Fmax= 8.79306e+03, atom=
>>> 7047
>>> Step= 2002, Dmax= 7.8e-03 nm, Epot= -2.66019e+06 Fmax= 3.31993e+03, atom=
>>> 7047
>>> Step= 2004, Dmax= 4.7e-03 nm, Epot= -2.66021e+06 Fmax= 3.95092e+03, atom=
>>> 7047
>>> Step= 2005, Dmax= 5.6e-03 nm, Epot= -2.66022e+06 Fmax= 4.76073e+03, atom=
>>> 7047
>>> Step= 2006, Dmax= 6.8e-03 nm, Epot= -2.66024e+06 Fmax= 5.70411e+03, atom=
>>> 7047
>>> Step= 2007, Dmax= 8.1e-03 nm, Epot= -2.66025e+06 Fmax= 6.84219e+03, atom=
>>> 7047
>>> Step= 2008, Dmax= 9.7e-03 nm, Epot= -2.66027e+06 Fmax= 8.21675e+03, atom=
>>> 7047
>>> Step= 2009, Dmax= 1.2e-02 nm, Epot= -2.66027e+06 Fmax= 9.84435e+03, atom=
>>> 7047
>>> Step= 2011, Dmax= 7.0e-03 nm, Epot= -2.66035e+06 Fmax= 9.95714e+02, atom=
>>> 7047
>>>
>>> writing lowest energy coordinates.
>>>
>>> Steepest Descents converged to Fmax < 1000 in 2012 steps
>>> Potential Energy = -2.6603498e+06
>>> Maximum force = 9.9571436e+02 on atom 7047
>>> Norm of force = 1.0860784e+01
>>>
>>> GROMACS reminds you: "Only entropy comes easy." (Anton Chekov)
>>> Is it a indication of proper minimization ?
>>>
>>> when I evaluated the energy of the system I found that the potential
>>> energy
>>> of the system is
>>> Steepest Descents converged to Fmax < 1000 in 2012 steps
>>> Potential Energy = -2.6603498e+06
>>> Maximum force = 9.9571436e+02 on atom 7047
>>> Norm of force = 1.0860784e+01
>>>
>> There is no error here. This is entirely normal output.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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