[gmx-users] GROMACS/ORCA QMMM

[Jose Tusell]

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?

Thanks,

Jose Tusell
On Mon, Nov 14, 2011 at 7:05 AM, Christoph Riplinger
<cri at thch.uni-bonn.de> wrote:
> Dear Jose,
>
> I tried oniom which stopped for me either (although without a segfault).
> Have you tried "QMMMscheme normal"?
>
> Christoph
>
> On 11/11/2011 05:53 PM, Jose Tusell wrote:
>>
>> Dear GROMACS users,
>>
>> I'm trying to run a QM-MM optimization.  I solvate my protein and add
>> ions then I do a classical optimization (just GROMACS).  After that I
>> run grompp with the following minim.mdp file (just showing qmmm
>> options):
>>
>> QMMM            = yes
>> QMMM-grps       = Other
>> QMmethod        = RHF
>> QMbasis         = 3-21G
>> QMMMscheme      = Oniom
>> QMcharge        = -1
>> QMmult          = 1
>> SH              = no
>>
>> This creates the *.tpr file that use to run mdrun.  I use the
>> following *.ORCAINFO file:
>>
>> !PAL8 Quick-DFT VerySlowConv
>> %scf
>>   Maxiter 300
>> end
>> %pal nprocs 8
>> end
>>
>> The ORCA run quickly converges but after that mdrun run stops with a
>> segmentation fault.  Am I missing something in all of this?  Any help
>> would be greatly appreciated.
>>
>> Thanks
>>
>> Jose Tusell
>
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