[gmx-users] GROMACS/ORCA QMMM

Christoph Riplinger cri at thch.uni-bonn.de
Sun Nov 20 21:19:43 CET 2011 

Dear Justin,

The LJ and LJ.Excl files should be generated when you set bOpt = yes. 
What does the .inp file say. Is there !QMMMOpt or only !EnGrad?
Christoph

On 11/18/2011 06:20 PM, Jose Tusell wrote:
> Hi Justin,
>
> I tried using a larger step size but my system blew up...  My guess is
> that I have a bad starting structure, I'll work on the initial
> structure for the QM region (energy minimize).
>
> When I'm running ORCA I want to have a LJ file to correct for the
> interaction of my QM system with the protein.  However this file is
> not created when I run QMMM, I've used the bOpt = true in the mdp
> file.  Can anyone please offer some help on how to create this LJ
> files?
>
> Thanks,
>
> Jose Tusell
>
> On Thu, Nov 17, 2011 at 2:07 PM, swati patel<swatipatel088 at gmail.com>  wrote:
>> hello,
>> I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated
>> Ligand topology from a sofware PRODRG using gromos87 force fields.After
>> solvating it,I am getting an error using grompp command
>>
>> Fatal error:
>> Atomtype HW not found
>>
>> can anyone provide me some help?
>>
>> Thanx with anticipation.
>>
>>
>> On Fri, Nov 18, 2011 at 2:29 AM, Jose Tusell<jrta1981 at gmail.com>  wrote:
>>> 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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