GMXFit

A python toolkit for fitting potential energy surface (PES) into gromacs format.

   

Code Organization

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Installation

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git clone https://github.com/masrul/GMXFit 
cd GMXFit
pip install . 

   

Functionalities

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• Read Gausssian .log/.out file and parse scanning data

• Fit scanning data into gromacs supported functions for

  • Dihedral
  • Angle

• Supported dihedral functions,

  • Fourier (DihFourier)
  • Rychart-Bellman (DihRB)

• Supported angle function,

  • Harmonic

• Convert TraPPE force field's function to gromacs format, supported functions,

  • Cosine-A
  • Cosine-C

   

Usages:

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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

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

Copyright

Masrul Huda (c) 2021