[gmx-users] GROMACS/ORCA QMMM
Justin A. Lemkul
jalemkul at vt.edu
Thu Nov 17 19:48:11 CET 2011
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
========================================
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