[gmx-users] Free Energy Calculations: Error during minimization step.
Wes Barnett
w.barnett at columbia.edu
Tue Sep 12 13:52:28 CEST 2017
On Tue, Sep 12, 2017 at 12:17 AM, Abhishek Acharya <abhi117acharya at gmail.com
> wrote:
> Just to add to the above post, running a none to vdw-q tranformation using
> the following parameters also results in the same error for simulation at
> first lambda.
>
Do you get this error on a normal simulation as well? That is, if you run
state 0 (with vdw and electrostatics on) without doing an free energy
calculations, do you still get the error? Perhaps you are using too big a
of a time step or your system is not equilibrated enough before using this
time step. Or you may just have a bad starting configuration.
>
> ************************************************************
> ************************************************************
> ********************************************************
> vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
> 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00
> coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15
> 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90
> 0.95 1.00
> ; We are not transforming any bonded or restrained interactions
> bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00
> restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00
> ; Masses are not changing (particle identities are the same at lambda = 0
> and lambda = 1)
> mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00
> ; Not doing simulated temperting here
> temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00
> ; Options for the decoupling
> sc-alpha = 0.5
> sc-coul = no ; linear interpolation of Coulomb (none
> in this case)
> sc-power = 1
> sc-sigma = 0.3
> couple-moltype = Protein ; name of moleculetype to decouple
> couple-lambda0 = none
> couple-lambda1 = vdw-q
> couple-intramol = no
> nstdhdl = 10
> ************************************************************
> ************************************************************
> ********************************************************
>
> Thanks in advance.
>
> Abhishek Acharya
> Research Associate,
> Department of Molecular Nutrition
> CSIR-Central Food Technological Research Institute,
> Mysuru-570020
>
> On Tue, Sep 12, 2017 at 9:42 AM, Abhishek Acharya <
> abhi117acharya at gmail.com>
> wrote:
>
> > Hello GROMACS users,
> >
> > As Wes had advised previously in this thread, the issue with the vdw
> > tranformations was rectified by removing the charges from the topology
> > file. Thereafter, I also tried running free energy calculations using the
> > following free-energy parameters:
> >
> > ************************************************************
> > ************************************************************
> > ********************************************************
> > free_energy = yes
> > init_lambda_state = 0
> > delta_lambda = 0
> > calc_lambda_neighbors = 1 ; only immediate neighboring windows
> > ; Vectors of lambda specified here
> > ; Each combination is an index that is retrieved from for each simulation
> > coul_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
> > 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00
> 1.00
> > 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00
> > 1.00 1.00
> > vdw_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10
> 0.15
> > 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85
> 0.90
> > 0.95 1.00
> > bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00
> > restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00
> > mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00
> > temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00
> > 0.00 0.00
> > ; Options for the decoupling
> > sc-alpha = 0.5
> > sc-coul = no ; linear interpolation of Coulomb
> > (none in this case)
> > sc-power = 1
> > sc-sigma = 0.3
> > couple-moltype = Protein ; name of moleculetype to decouple
> > couple-lambda0 = vdw-q
> > couple-lambda1 = none
> > couple-intramol = no
> > nstdhdl = 10
> >
> > ************************************************************
> > ************************************************************
> > ********************************************************
> >
> > As you can see, I want to first annihilate the charges, followed by a vdw
> > tranformation, using a total of 41 lambdas. Since both charges and vdw
> are
> > being interpolated, the topology files contain the normal charges for the
> > transformed molecule. This setup is similar to what Wes had suggested in
> a
> > previous response to this thread.
> >
> > The issue is that I am facing the exactly the same error in minimization
> > step at final lambda state where both vdw and electrostatics are turned
> off.
> >
> > ------------------------------------------------------------
> > ------------------------------------------------------------
> > ------------------------------------------------------
> > Program gmx mdrun, VERSION 5.1.2
> > Source code file: /home/bp-lab/Downloads/gromacs-5.1.2/src/gromacs/
> mdlib/constr.cpp,
> > line: 555
> >
> > Fatal error:
> >
> > step 10: Water molecule starting at atom 120 can not be settled.
> > Check for bad contacts and/or reduce the timestep if appropriate.
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > ------------------------------------------------------------
> > ------------------------------------------------------------
> > -------------------------------------------------------
> >
> > Now, what I understood is that in case of just the vdw transformation,
> > since we are not calculating any electrostatics, the charges should be
> zero
> > in topology file. Whereas, in case of just the charge transformation, the
> > charges are required in the topology file as charges are interpolated in
> > this step. And performing the simulation as such give no errors.
> >
> > I do not understand why the error is surfacing in case of a [vdw-q] to
> > [none ] tranformation., especially now that the charges are gradually
> > decoupled prior to decoupling the vdw interactions. Any help will be
> > greatly appreciated.
> >
> > Sincerely,
> > Abhishek
> >
> >
> > Abhishek Acharya
> > Research Associate,
> > Department of Molecular Nutrition
> > CSIR-Central Food Technological Research Institute,
> > Mysuru-570020
> >
> > On Sun, Sep 10, 2017 at 8:02 AM, Abhishek Acharya <
> > abhi117acharya at gmail.com> wrote:
> >
> >>
> >>
> >>
> >> You can do them separately, but the charges need to have been turned off
> >> for the molecule you are transforming for the second step when turning
> off
> >> vdw. In other words, all charges must be 0.0 for the molecule in the
> >> topology file for the vdw transformation. Is that what you've done?
> >>
> >> Justin's tutorial gives an explanation on why this needs to be done, and
> >> in
> >> his topology he had all charges at 0.0 in the methane topology file.
> >>
> >>
> >> Okey, one thing that I presumed while performing the second
> >> transformation is that it is sufficient to 'turn-off' charge
> electrostatics
> >> just by stating c-lambda0=none and c-lambda1 = vdw (or vice-versa). It
> >> doesn't matter if the topology files have the charges or not.
> Therefore, i
> >> had included the charges in my topology file.
> >>
> >> Then this explains the problem in my case. Thank you so much Wes for
> >> clarifying that out.
> >>
> >> Sincerely,
> >> Abhishek Acharya
> >>
> >>
> >>
> >
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--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu
http://wbarnett.us
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