[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
>
> ========================================
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