[gmx-users] minimization_error
Bratin Kumar Das
177cy500.bratin at nitk.edu.in
Sun Sep 9 21:20:58 CEST 2018
Thank you sir for clearing my doubt.
On Mon, Sep 10, 2018 at 12:44 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/9/18 3:12 PM, Bratin Kumar Das wrote:
>
>> Respected Dr. Justin,
>> When I run the gmx energy command I
>> found
>> potential energy in positive
>> Energy Average Err.Est. RMSD Tot-Drift
>> ------------------------------------------------------------
>> -------------------
>> Potential 4.67273e+08 4.7e+08 1.83206e+10 -2.80745e+09
>> (kJ/mol)
>> In first mail I wrote wrong. So my average potential energy is coming
>> 4.62e+08, I think it is not acceptable for subsequent equilbration.
>> and when the minimization started some of the atom has high potential
>> energy
>>
>> 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
>> upto 6th step the potential energy was positive.
>>
>
> That's what energy minimization does - it relaxes a system from a point
> high on the potential energy surface to one that is low on the potential
> energy surface. The average energy during EM is meaningless.
>
>
> -Justin
>
> On Mon, Sep 10, 2018 at 12:32 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> 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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
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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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> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
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