[gmx-users] GROMACS/ORCA QMMM
Justin A. Lemkul
jalemkul at vt.edu
Mon Nov 21 06:00:38 CET 2011
Jose Tusell wrote:
> When I run gromacs with bOpt yes I run into the a problem with the
> coordinates of my qm system: the initial coordinates are the
> following:
>
> NAME = ybu_em_qmmm.inp
> | 1> #input-file generated by gromacs
> | 2> !QMMMOpt TightSCF
> | 3> !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym
> | 4> %scf
> | 5> Maxiter 5000
> | 6> end
> | 7> %pal nprocs 8
> | 8> end
> | 9>
> | 10>
> | 11>
> | 12> %LJCOEFFICIENTS "ybu_em_qmmm.LJ"
> | 13> *xyz -2 1
> | 14> 7 46.4499998 40.2500010 48.1099987
> | 15> 6 45.2400017 40.2899981 47.5600004
> | 16> 7 44.7599983 40.6899977 46.3600016
> | 17> 6 43.4700012 40.5999994 46.0599995
> | 18> 7 42.6300001 40.1100016 46.9500017
> | 19> 6 43.0100012 39.6799994 48.1699991
> | 20> 7 42.1299982 39.1499996 49.0199995
> | 21> 1 42.4300003 38.8100004 49.9200010
> | 22> 1 41.1600018 39.0899992 48.7699986
> | 23> 6 44.3400002 39.7700000 48.4999990
> | 24> 7 45.0799990 39.4600010 49.5800018
> | 25> 6 46.3500023 39.7600007 49.3499994
> | 26> 6 47.7699995 40.5399990 47.4900007
> | 27> 8 48.8000011 41.0900021 48.3400011
> | 28> 6 49.8199987 41.7100000 47.4800014
> | 29> 6 47.7400017 41.5500021 46.3600016
> | 30> 8 46.9999981 41.4499998 45.1499987
> | 31> 1 47.2300005 40.5999994 44.6799994
> | 32> 6 49.1900015 41.9199991 46.1000013
> | 33> 8 49.7800016 40.8699989 45.3399992
> | 34> 1 50.7399988 41.0900021 45.1599979
> | 35> 6 50.0799990 43.2399988 47.5799990
> | 36> 8 51.4400005 43.5300016 47.9400015
> | 37> 15 51.8400002 43.3099985 49.4799995
> | 38> 8 52.1000004 44.8099995 49.9800014
> | 39> 8 50.5700016 42.5000000 50.0600004
> | 40> 8 53.1099987 42.3299980 49.3599987
> | 41> 15 54.4700003 43.1799984 49.4500017
> | 42> 8 55.5600023 42.1400023 48.8899994
> | 43> 8 54.1200018 44.4799995 48.5599995
> | 44> 8 54.5300007 43.5900021 50.9999990
> | 45> 15 55.8799982 43.3500004 51.8499994
> | 46> 8 57.0900011 43.9900017 50.9899998
> | 47> 8 55.8300018 43.9099979 53.2200003
> | 48> 8 56.1399984 41.7600012 51.8499994
> | 49> 1 43.1099987 40.9200001 45.1000023
> | 50> 1 47.1600008 39.6399999 50.0400019
> | 51> 1 48.1400013 39.6199989 47.0900011
> | 52> 1 47.3199987 42.4200010 46.8200016
> | 53> 1 49.3300009 42.8999996 45.7000017
> | 54> 1 50.7200003 41.1499977 47.4200010
> | 55> 1 49.8600006 43.6999989 46.6300011
> | 56> 1 49.4299984 43.6600018 48.3199978
> | 57> 12 51.3999987 43.3799982 51.9299984
> | 58> *
> | 59> %pointcharges "ybu_em_qmmm.pc"
> | 60>
> | 61>
> | 62> ****END OF INPUT****
>
> This first calculation doesn't run into problems however after this
> the new coordinates are wrong by a factor of 10.
>
> This is the next input file generated by gromacs:
>
> NAME = ybu_em_qmmm.inp
> | 1> #input-file generated by gromacs
> | 2> !QMMMOpt TightSCF
> | 3> !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym
> | 4> %scf
> | 5> Maxiter 5000
> | 6> end
> | 7> %pal nprocs 8
> | 8> end
> | 9>
> | 10>
> | 11>
> | 12> %LJCOEFFICIENTS "ybu_em_qmmm.LJ"
> | 13> *xyz -2 1
> | 14> 7 4.6643215 4.0067959 4.8652828
> | 15> 6 4.4694147 4.0687612 4.6910113
> | 16> 7 4.4788954 4.0736303 4.5814043
> | 17> 6 4.2882785 4.0960234 4.5192298
> | 18> 7 4.1568694 3.9851558 4.6636197
> | 19> 6 4.2702511 3.9942223 4.8413402
> | 20> 7 4.1388491 3.8647231 4.9325246
> | 21> 1 4.2422304 3.8729668 5.0225985
> | 22> 1 4.0874949 3.9029175 4.8758829
> | 23> 6 4.4479644 3.9264068 4.8907641
> | 24> 7 4.4724247 3.8935867 5.0617158
> | 25> 6 4.6581322 3.9623603 4.9860328
> | 26> 6 4.7224784 3.9516553 4.7729388
> | 27> 8 4.9013394 4.1037330 4.9433815
> | 28> 6 5.0506485 4.1505158 4.7845429
> | 29> 6 4.7479546 4.2596489 4.5867884
> | 30> 8 4.6396983 4.1753584 4.3912268
> | 31> 1 4.7245148 4.0333679 4.4395000
> | 32> 6 4.9467531 4.1628179 4.5303190
> | 33> 8 5.0127959 4.0332937 4.4357231
> | 34> 1 5.0972128 4.1086709 4.5025694
> | 35> 6 4.9707726 4.4155064 4.7358957
> | 36> 8 5.1747119 4.3822494 4.7240046
> | 37> 15 5.1759595 4.3526104 4.9696961
> | 38> 8 5.2000558 4.5951414 5.0385225
> | 39> 8 4.9872991 4.2056358 5.0856835
> | 40> 8 5.3196424 4.1316289 4.9306369
> | 41> 15 5.4781163 4.3365851 4.9144840
> | 42> 8 5.6436682 4.1501650 4.8309124
> | 43> 8 5.4556131 4.5460758 4.7758737
> | 44> 8 5.4388809 4.3959689 5.1872373
> | 45> 15 5.6339312 4.3419433 5.2184927
> | 46> 8 5.8053279 4.4479111 5.0789297
> | 47> 8 5.5981785 4.4297397 5.4245871
> | 48> 8 5.6559128 4.0851763 5.2241915
> | 49> 1 4.2944524 4.1013804 4.4863331
> | 50> 1 4.7380015 3.9515409 5.0357658
> | 51> 1 4.8261809 3.9258796 4.7002071
> | 52> 1 4.7115117 4.2592505 4.6899751
> | 53> 1 4.9388400 4.3221569 4.5484522
> | 54> 1 5.1027077 4.0887082 4.7342393
> | 55> 1 4.9870053 4.3987840 4.6446544
> | 56> 1 4.9254298 4.3886098 4.8489299
> | 57> 12 5.1316565 4.3423077 5.2266484
> | 58> *
> | 59> %pointcharges "ybu_em_qmmm.pc"
> | 60>
> | 61>
> | 62> ****END OF INPUT****
>
> Any ideas why this is happening?
>
A factor of 10 would seem to me to be an Angstrom -> nm conversion.
-Justin
> Thanks,
>
> Jose Tusell
>
> On Sun, Nov 20, 2011 at 5:03 PM, Jose Tusell <jrta1981 at gmail.com> wrote:
>> 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
>>>>>>>>>>
>>>>>>>>>> ========================================
>>>>>>>>>> --
>>>>>>>>>> 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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>>>>>>> --
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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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