A python toolkit for fitting potential energy surface (PES) into gromacs format.
git clone https://github.com/masrul/GMXFit
cd GMXFit
pip install .
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Read Gausssian .log/.out file and parse scanning data
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Fit scanning data into gromacs supported functions for
- Dihedral
- Angle
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Supported dihedral functions,
- Fourier (DihFourier)
- Rychart-Bellman (DihRB)
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Supported angle function,
- Harmonic
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Convert TraPPE force field's function to gromacs format, supported functions,
- Cosine-A
- Cosine-C
Neccessary files are located in Examples/.
Case-1: Fitting dihedral from gaussian output
from GMXFit.GaussIO import GaussScan
from GMXFit.FitPES import DihedralFit
# Create Data object from gaussian output file
gauss = GaussScan("dihedral_scan.log")
# Pass data object to PES Fitter
dihFit = DihedralFit(gauss)
# Fit to Rychart-Bellman
dihFit.Fit(fitType="DihRB", drawPES=True)Result
Scanned dihedral [D20] : 5-4-9-11
o FitType: Rychart-Bellman
o Coefficients: 9.07027814 -0.80408665 -22.42055866 -0.42059325 16.59787317 -1.05822607
o R-sqaure: 0.999 |
|---|
| Fig-1: PES Fitting Gaussian log to Gromacs dihedral form |
Case-2: Fitting angle from gaussian output
from GMXFit.GaussIO import GaussScan
from GMXFit.FitPES import AngleFit
# Create Data object from gaussian output file
gauss = GaussScan("angle_scan.log")
# Pass data object to PES Fitter
angFit = AngleFit(gauss)
# Fit
angFit.Fit()Result
Scanned angle [A15] : 4-9-11
o FitType: Angle Harmonic
o Force constant: 765.97905760 kJ/mol/nm^2
o Equilibrium angle: 120.56
o R-sqaure: 1.000 |
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| Fig-2: PES Fitting Gaussian log to Gromacs Angle Form |
Case-3: Converting TraPPE dihedral type to gromacs type
from GMXFit.TraPPE import TrappePES
from GMXFit.FitPES import DihedralFit
# Create a TrappePES object
trappe_pes = TrappePES()
# collect coeffs from TraPPE website/literature
trappe_coeffs = (0.00, 355.03, -68.19, 791.32)
trappe_funType = "CosineA" # CosineC is also supported
# Pass function type and coeffs to create PES
trappe_pes.createPES(dihType=trappe_funType, coeffs=trappe_coeffs)
# Pass data object to PES Fitter
dihFit = DihedralFit(trappe_pes)
# Fit
dihFit.Fit(fitType="DihFourier", drawPES=True)Result
o FitType: Fourier
o Coefficients: 5.90355244 -1.13388515 13.15832217 0.00000002
o R-sqaure: 1.000 |
|---|
| Fig-3: PES Fitting TraPPE to Gromacs |
Masrul Huda (c) 2021