[gmx-users] GROMACS/ORCA QMMM
Jose Tusell
jrta1981 at gmail.com
Mon Nov 21 00:57:31 CET 2011
I've tried the bOpt = true. Is the flag bOpt = yes? I'll try that
and I'll let you know.
Ramon
On Sun, Nov 20, 2011 at 1:19 PM, Christoph Riplinger
<cri at thch.uni-bonn.de> wrote:
> 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
>>>>>>>
>>>>>>> ========================================
>>>>>>> --
>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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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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