[gmx-users] GROMACS/ORCA QMMM
Jose Tusell
jrta1981 at gmail.com
Fri Nov 18 18:20:32 CET 2011
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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