[gmx-users] GROMACS/ORCA QMMM
Jose Tusell
jrta1981 at gmail.com
Thu Nov 17 21:59:23 CET 2011
I'll try changing the step size first and if that fails I'll try
another algorithm. Thanks for the input.
Jose Tusell
On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Jose Tusell wrote:
>>
>> Hi Justin,
>>
>> Thanks for the input on why this is happening. It sounds a little
>> suspicious that the energy doesn't change after a few steps of energy
>> minimization. Do you know of any way that I can find out what is
>> going on?
>>
>
> The screen output should indicate the atom with maximal force. Sometimes
> the EM algorithms get stuck when the geometry cannot change without making
> detrimental moves. You either need a larger step size, a different
> algorithm, or a better starting structure, if that is the case. I have seen
> this many times before, nothing suspicious about it.
>
> -Justin
>
>> Thanks,
>>
>> Jose Tusell
>>
>> On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul <jalemkul at vt.edu>
>> wrote:
>>>
>>> Jose Tusell wrote:
>>>>
>>>> Hi Cristoph,
>>>>
>>>> Thanks for the reply. I found that my problem was not gromacs. The
>>>> input that ORCA was receiving from GROMACS did not have the correct
>>>> number of hydrogens. I've solved this problem now and ORCA is running
>>>> fine. I however ran into another problem with my energy minimization.
>>>> The output from my gromacs log file is the following:
>>>>
>>>> Step Time Lambda
>>>> 0 0.00000 0.00000
>>>>
>>>> Energies (kJ/mol)
>>>> Bond Angle Proper Dih. Improper Dih.
>>>> LJ-14
>>>> 1.21899e+04 1.92496e+03 5.62567e+03 1.49141e+01
>>>> 3.68001e+03
>>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum
>>>> En.
>>>> 2.41200e+04 1.47494e+05 -5.06544e+05 -7.56009e+04
>>>> -3.96508e+06
>>>> Potential Pressure (bar)
>>>> -4.35218e+06 -2.10629e+04
>>>>
>>>> Step Time Lambda
>>>> 1 1.00000 0.00000
>>>>
>>>> Energies (kJ/mol)
>>>> Bond Angle Proper Dih. Improper Dih.
>>>> LJ-14
>>>> 1.20006e+04 1.92297e+03 5.62600e+03 1.47801e+01
>>>> 3.67746e+03
>>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum
>>>> En.
>>>> 2.41174e+04 1.46421e+05 -5.06609e+05 -7.56156e+04
>>>> -4.00402e+06
>>>> Potential Pressure (bar)
>>>> -4.39246e+06 -2.10739e+04
>>>>
>>>> Step Time Lambda
>>>> 2 2.00000 0.00000
>>>>
>>>> Energies (kJ/mol)
>>>> Bond Angle Proper Dih. Improper Dih.
>>>> LJ-14
>>>> 1.17961e+04 1.92126e+03 5.62633e+03 1.46477e+01
>>>> 3.67461e+03
>>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum
>>>> En.
>>>> 2.41145e+04 1.45528e+05 -5.06679e+05 -7.56315e+04
>>>> -4.18671e+06
>>>> Potential Pressure (bar)
>>>> -4.57635e+06 -2.10854e+04
>>>>
>>>> Step Time Lambda
>>>> 3 3.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 4 4.00000 0.00000
>>>>
>>>> Energies (kJ/mol)
>>>> Bond Angle Proper Dih. Improper Dih.
>>>> LJ-14
>>>> 1.16705e+04 1.92041e+03 5.62652e+03 1.45728e+01
>>>> 3.67282e+03
>>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum
>>>> En.
>>>> 2.41128e+04 1.45113e+05 -5.06721e+05 -7.56410e+04
>>>> -4.24486e+06
>>>> Potential Pressure (bar)
>>>> -4.63509e+06 -2.10913e+04
>>>>
>>>> Step Time Lambda
>>>> 5 5.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 6 6.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 7 7.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 8 8.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 9 9.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 10 10.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 11 11.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 12 12.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 13 13.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 14 14.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 15 15.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 16 16.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 17 17.00000 0.00000
>>>>
>>>> Step Time Lambda
>>>> 18 18.00000 0.00000
>>>>
>>>>
>>>> Stepsize too small, or no change in energy.
>>>> Converged to machine precision,
>>>> but not to the requested precision Fmax < 1000
>>>>
>>>> Double precision normally gives you higher accuracy.
>>>> You might need to increase your constraint accuracy, or turn
>>>> off constraints alltogether (set constraints = none in mdp file)
>>>>
>>>> Why doesn't GROMACS output the energies for certain steps? Step 3 and
>>>> steps 5-18 do show any output in the log file. Any ideas why this is
>>>> happening?
>>>>
>>> This happens for the reasons printed by mdrun - those steps caused no
>>> change
>>> in energy.
>>>
>>> -Justin
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
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>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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