[gmx-users] GROMACS/ORCA QMMM

[Jose Tusell]

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?

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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