[gmx-users] GROMACS/ORCA QMMM

[Justin A. Lemkul]

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

========================================