[gmx-users] GROMACS/ORCA QMMM
Jose Tusell
jrta1981 at gmail.com
Mon Nov 21 01:03:00 CET 2011
That solved it. In the ORCA manual for version 2.8 it says to use
bOpt = true instead of bOpt = yes. And there is no mention of the mdp
option in the gromacs manual or gromacs online mdp options.
Ramon
On Sun, Nov 20, 2011 at 4:57 PM, Jose Tusell <jrta1981 at gmail.com> wrote:
> 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
>>>>>>>>
>>>>>>>> ========================================
>>>>>>>> --
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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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