Package: gmxpy
gmxpyAuthor: Goosang YuContact:gsyu93@gmali.comWrapping GROMACS by python script for meSince 2023. 07. 12.Tested GROMCAS ver. 2023.1InstallationpipinstallgmxpyThis package does not include GROMACS. You need to install GROMCAS separately. Also, gmxpy is currently being developed based on GROMACS version 2023.1. If you use a version that is too old, it may not be compatible.You don need to use XMGRACE anymore!GROMACS by default generates graphs of data in the form of xmgrace files (.xvg). Xmgrace produces visually appealing plots, but it can be cumbersome to handle in different languages or operating systems. The most important thing is that I am not familiar with it.One of the functions included in gmxpy, called 'xvg2df', converts it into a much simpler DataFrame format.importgmxpyasgmxdf_xvg=gmx.xvg2df('interaction_energy.xvg')df_xvg()Coul-SR:Protein-JZ4LJ-SR:Protein-JZ4Time (ps)0-15.2106-98.938210-15.5369-108.83420-26.0345-105.19330-13.2364-108.94840-13.0772-109.427With just a little additional effort, it can be conveniently plotted and visualized as a graph. I have freely chosen the colors that I personally like.df_xvg().plot()Make dataframe from gmx_MMPBSA results fileWhen you done your MMPB(GB)SA bygmx_MMPBSA, you will get data file containing decomposition results (DECOMP_MMPBSA_YOURSAMPLE.dat)| Run on Fri Oct 27 19:17:14 2023\n
| GB non-polar solvation energies calculated with gbsa=2
idecomp = 3: Pairwise decomp adding 1-4 interactions to Internal.
Energy Decomposition Analysis (All units kcal/mol): Generalized Born model

DELTAS:
Total Energy Decomposition:
Resid 1,Resid 2,Internal,,,van der Waals,,,Electrostatic,,,Polar Solvation,,,Non-Polar Solv.,,,TOTAL,,
,,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean
R:A:ARG:351,R:A:ARG:351,0.0,0.0,0.0,0.0,0.5897586551665688,0.015222429700453965,0.0,6.785105251173467,0.1751322965612053,2.9772637441705534,3.1993571192946018,0.08257952368898057,1.0425542756210526,0.6088115226883254,0.01571420872548597,4.019818019791606,7.549305000315245,0.19485727534109232
R:A:ARG:351,R:A:ASN:355,0.0,0.0,0.0,0.0,0.1863456749011414,0.0048098216301125886,0.0,0.6239917901458101,0.016106030960193803,0.01945755229846769,0.6328086828777381,0.016333606305824484,0.0033432117553630915,0.135970829538314,0.0035095820567055645,0.022800764053830778,0.9181641249441898,0.023698997416992967
...This file need somethigng arrange for analysis... so I make functionmake_decomp_dffor this.fromgmxpy.analysisimportmake_decomp_dfdf_decomp=make_decomp_df('DECOMP_MMPBSA_8SSN_K294E')df_decompResid 1Resid 2Internal_Avg.Internal_Std. Dev.Internal_Std. Err. of Meanvan der Waals_Avg.van der Waals_Std. Dev.van der Waals_Std. Err. of MeanElectrostatic_Avg.Electrostatic_Std. Dev.Electrostatic_Std. Err. of MeanPolar Solvation_Avg.Polar Solvation_Std. Dev.Polar Solvation_Std. Err. of MeanNon-Polar Solv._Avg.Non-Polar Solv._Std. Dev.Non-Polar Solv._Std. Err. of MeanTOTAL_Avg.TOTAL_Std. Dev.TOTAL_Std. Err. of MeanR:A:ARG:351R:A:ARG:35100000.5897590.01522206.7851050.1751322.9772643.1993570.082581.0425540.6088120.0157144.0198187.5493050.194857R:A:ARG:351R:A:ASN:35500000.1863460.0048100.6239920.0161060.0194580.6328090.0163340.0033430.1359710.003510.0228010.9181640.023699R:A:ARG:351R:A:ALA:35600000.0161110.00041600.2201860.005683-0.009270.2306230.0059530.0000060.0016660.000043-0.009260.3192670.008241R:A:ARG:351R:A:VAL:35700000.0036770.00009500.1145680.002957-0.002830.115020.002969000-0.002830.1623850.004191R:A:ARG:351R:A:LEU:35900000.0223950.00057800.2773920.00716-0.021040.2905590.00750.0000310.0037920.000098-0.021010.4023510.010385............................................................L:B:AY7:527R:A:PHE:516000-0.205270.1076020.002777-0.038280.028270.000730.0779290.0307340.000793-0.057290.056160.00145-0.222910.1283590.003313L:B:AY7:527R:A:ILE:521000-0.683360.2185840.005642-0.171550.1316630.0033980.1993710.1185690.00306-0.515610.130990.003381-1.171140.3103720.008011L:B:AY7:527R:A:SER:522000-0.095440.0551330.001423-0.085890.1231550.0031790.1021060.1165480.003008-0.004090.022690.000586-0.083320.1797360.004639L:B:AY7:527R:A:VAL:525000-1.60840.8125590.020973-0.481980.9611920.024810.3323010.4422810.011416-1.149920.5845040.015087-2.908011.4565020.037594L:B:AY7:527L:B:AY7:52700002.4649590.06362402.8343870.07315914.783211.8782810.0484819.88720.6498120.01677224.670414.2497020.10969