[gmx-users] Free Energy Calculations: Error during minimization step.
Abhishek Acharya
abhi117acharya at gmail.com
Tue Sep 12 06:17:25 CEST 2017
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.
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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
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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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