[gmx-users] minimization_error

Justin Lemkul jalemkul at vt.edu
Sun Sep 9 21:14:19 CEST 2018



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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
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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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