Yes. But where does the code go wrong? I'm reading the qm_orca.c
file but I can't seem to know exactly were the factor of 10 is not
accounted for. I see the factor of ten when going from gromacs to
orca in (lines 219 to 221 of qm_orca.c file):
qm->xQM[i][XX]/0.1,
qm->xQM[i][YY]/0.1,
qm->xQM[i][ZZ]/0.1);
I just don't know where to look for the factor of 10 in the code.
Could anyone point me to this?
Thanks,
Jose Tusell
On Sun, Nov 20, 2011 at 10:00 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
>
>
> 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 <jrta1...@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 <jrta1...@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
>>>> <c...@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<swatipatel...@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<jrta1...@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<jalem...@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<jalem...@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@gromacs.org
>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>>>> Please search the archive at
>>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before
>>>>>>>>>>> posting!
>>>>>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>>>>>> interface
>>>>>>>>>>> or send it to gmx-users-requ...@gromacs.org.
>>>>>>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> ========================================
>>>>>>>>>
>>>>>>>>> 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@gromacs.org
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>> Please search the archive at
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>>>>>>>> --
>>>>>>>> gmx-users mailing list gmx-users@gromacs.org
>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>>>>> gmx-users mailing list gmx-users@gromacs.org
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>>>>> gmx-users mailing list gmx-users@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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