### Install ForceBalance from Source Source: https://github.com/leeping/forcebalance/blob/master/README.txt Installs the ForceBalance package after building from source. Use --user or --prefix for local installations. ```bash python setup.py install ``` ```bash python setup.py install --user ``` ```bash python setup.py install --prefix=$HOME/.local ``` ```bash python setup.py install --prefix=/your/favorite/directory export PYTHONPATH=/your/favorite/directory ``` -------------------------------- ### Install libxml2 and libxslt Development Headers on Ubuntu Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Install the required development headers for libxml2 and libxslt on Ubuntu systems, which are prerequisites for installing lxml. ```bash sudo apt-get install libxml2-dev libxslt1-dev ``` -------------------------------- ### Install ForceBalance with Pip Source: https://github.com/leeping/forcebalance/blob/master/README.txt Installs ForceBalance from the Python Package Index (PyPI). ```bash pip install forcebalance ``` -------------------------------- ### Install BLAS Development Headers on Ubuntu Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Install the necessary BLAS libraries and headers on Ubuntu systems to facilitate the installation of SciPy. ```bash sudo apt-get install libblas-dev ``` -------------------------------- ### Install GLib and FFTW on Ubuntu/Debian Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Use this command to install the development libraries for GLib and FFTW on Ubuntu or Debian-based systems. ```bash sudo apt-get install libglib2.0-dev libfftw3-dev ``` -------------------------------- ### Copy Setup Files to Simulation Directories Source: https://github.com/leeping/forcebalance/blob/master/studies/009_voelz_nspe/Nspe_2/About_VAV.txt Copies generated topology and coordinate files from the Setup directory to the appropriate locations within the simulation directories. This organizes files for the ForceBalance run. ```bash cd .. mkdir forcefield cp Setup/molecule.itp forcefield mkdir -p simulations/2dscan cp Setup/all.gro !$ cp Setup/qdata.txt !$ mkdir simulations/2dscan/settings cp Setup/shot.mdp !$ cp Setup/topol.top !$ ``` -------------------------------- ### GitHub Release Notes Example Source: https://github.com/leeping/forcebalance/wiki/Home Example of release notes for a GitHub release, detailing changes since the previous version. Use markdown for formatting. ```markdown # Minor changes and bugfixes since v1.9.2 * Update CI, fix compatibility with OpenMM 7.7 by @mattwthompson in https://github.com/leeping/forcebalance/pull/249 * Cache generate_conformers with hash_molecule_args_and_kwargs approach by @mattwthompson in https://github.com/leeping/forcebalance/pull/251 * Change molecule.qm_bondorder into a list of bond order matrices for all frames by @leeping in https://github.com/leeping/forcebalance/commit/a8659b20979c405f192d589e5bdbb606dc6ea641 **Full Changelog**: https://github.com/leeping/forcebalance/compare/v1.9.2...v1.9.3 ``` -------------------------------- ### Install ForceBalance to Custom Location Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Install the package to a specified directory, such as /home/leeping/local, when root permissions are unavailable or a custom location is preferred. ```bash python setup.py install --prefix=/home/leeping/local ``` -------------------------------- ### ForceBalance Directory Structure Example Source: https://github.com/leeping/forcebalance/blob/master/doc/usage.txt An example of the directory structure required for a ForceBalance job. It includes directories for force fields, targets, temporary files, and results. ```text +- forcefield | |- water.itp +- targets | +- cluster-02 | | +- settings (contains job settings) | | | |- shot.mdp | | | |- topol.top | | |- all.gro (contains geometries) | | |- qdata.txt (contains QM data) | +- cluster-03 | | +- settings | | | |- shot.mdp | | | |- topol.top | | |- all.gro | | |- qdata.txt | +- |- input.in +- temp | |- iter_0001 | |- iter_0002 | | |- +- result | |- water.itp (Optimized force field, generated on completion) |- input.in (ForceBalance input file) ``` -------------------------------- ### Install lxml to Custom Location Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Install the lxml package to a custom prefix after successful configuration. This step requires Python to be compiled with --enable-shared. ```bash python setup.py install --prefix=$HOME/local ``` -------------------------------- ### Install ForceBalance Source: https://github.com/leeping/forcebalance/blob/master/src/tests/About.txt Install or reinstall ForceBalance to ensure tests are run with the latest file versions. This is recommended before running the test suite. ```bash python setup.py install ``` -------------------------------- ### GitHub Release Title Example Source: https://github.com/leeping/forcebalance/wiki/Home Example of a release title for a GitHub release. Ensure the version number is accurate. ```text Version 1.9.3 Minor Release ``` -------------------------------- ### Tag ITP File for Parameterization Source: https://github.com/leeping/forcebalance/blob/master/studies/009_voelz_nspe/Nspe_2/About.txt This example shows how to tag specific lines in an .itp file to indicate which parameters, such as dihedral Fourier coefficients, should be subject to parameterization by ForceBalance. ```text hc c3 c n 9 180.00 0.00000 2 ; PARM 6 hc c3 c3 n 9 0.00 0.65270 3 ; PARM 6 ``` -------------------------------- ### Run ForceBalance Optimization Source: https://github.com/leeping/forcebalance/blob/master/doc/tutorial.txt Execute the ForceBalance optimization process using a specified input file. Ensure ForceBalance is installed and the input file is correctly configured. ```bash ForceBalance.py very_simple.in ``` -------------------------------- ### Run All Tests Source: https://github.com/leeping/forcebalance/blob/master/src/tests/About.txt Execute all tests and print results to standard output. Ensure ForceBalance is installed before running. ```bash python test ``` -------------------------------- ### Install NumPy using pip Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt A simple command to install the NumPy package using pip, which can help resolve dependency issues. ```bash pip install numpy ``` -------------------------------- ### Build PDF Manual with LaTeX Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Command to build the PDF manual from the generated LaTeX files. Requires a LaTeX distribution to be installed. ```bash make ``` -------------------------------- ### Install ForceBalance with Conda Source: https://github.com/leeping/forcebalance/blob/master/README.txt Installs ForceBalance and its core dependencies using the conda-forge channel. Optional dependencies are not included. ```bash conda install --strict-channel-priority -c conda-forge forcebalance ``` -------------------------------- ### Install GLib and FFTW on CentOS/Yum Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Use this command to install the development libraries for GLib and FFTW on CentOS or other distributions using the yum package manager. Adjust architecture if necessary. ```bash sudo yum install glib2-devel.x86_64 fftw3-devel.x86_64 ``` -------------------------------- ### ForceBalance Optimizer Start Source: https://github.com/leeping/forcebalance/blob/master/doc/tutorial.txt Indicates the beginning of the main optimization loop in ForceBalance. It specifies the optimization mode, such as Newton-Raphson with an adaptive radius. ```text #========================================================# #| Main Optimizer |# #| Newton-Raphson Mode (Adaptive Radius) |# #========================================================# ``` -------------------------------- ### Copy AMBER-FB15 Parameters to Gromacs Installation Source: https://github.com/leeping/forcebalance/blob/master/Products/AMBER-FB15/About.txt Copy the amberfb15.ff folder to the Gromacs installation's top directory to make AMBER-FB15 a menu choice in pdb2gmx. ```bash cp -r FinalParams/GMX/amberfb15.ff $HOME/opt/gromacs/share/gromacs/top/ ``` -------------------------------- ### Configure Environment with Anaconda2 Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Add the Anaconda2 bin directory to your PATH to resolve dependency issues. Assumes Anaconda2 is installed in /home/leeping/opt/anaconda2. ```bash export PATH=/home/leeping/opt/anaconda2/bin:$PATH ``` -------------------------------- ### Configure lxml Build with Custom Prefix Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Configure the lxml build process to install into a custom directory, ensuring compatibility with Python compiled with shared libraries. ```bash ./configure --prefix=$HOME/local --with-python=$HOME/local ``` -------------------------------- ### Collect Structure Files with Python Source: https://github.com/leeping/forcebalance/blob/master/studies/009_voelz_nspe/Nspe_2/About_VAV.txt Concatenates all structure files into a single file for convenience. This script is part of the setup process. ```bash python collect.py ``` -------------------------------- ### Configure Environment with Enthought Python Distribution (EPD) Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Set up your environment variables to use EPD, which includes necessary packages like SciPy and lxml. Assumes EPD is installed in /home/leeping/opt/epd-7.3.2. ```bash export PATH=/home/leeping/opt/epd-7.3.2/bin:$PATH export PYTHONUSERBASE=/home/leeping/opt/epd-7.3.2 ``` -------------------------------- ### Add Custom Python Module Location (Symlink) Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Create a symbolic link to make Python recognize modules installed in a custom location. ```bash ln -s /home/leeping/local /home/leeping/.local ``` -------------------------------- ### Extract ForceBalance Tarball Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Extracts the ForceBalance source code from a downloaded tar.gz archive. This is the first step when installing from source. ```bash tar xvzf ForceBalance-[version].tar.gz ``` -------------------------------- ### Add Custom Python Module Location (PYTHONUSERBASE) Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Set the PYTHONUSERBASE environment variable to point to your custom installation directory. This is an alternative to using symlinks. ```bash export PYTHONUSERBASE=/home/leeping/local ``` -------------------------------- ### Resize Image for Web Source: https://github.com/leeping/forcebalance/blob/master/doc/Images/convert-images.txt Use this command to resize an image to a specific width while maintaining aspect ratio, suitable for web display. Ensure the 'convert' utility is installed and accessible. ```bash convert -resize 400 cycle.png cycle_sm.png ``` -------------------------------- ### Set ATLAS Environment Variable Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Configure the ATLAS environment variable to point to the installed ATLAS library, used for compiling SciPy. ```bash export ATLAS=$HOME/local/lib/libatlas.so ``` -------------------------------- ### ForceBalance Validation Output Example Source: https://github.com/leeping/forcebalance/blob/master/doc/tutorial.txt This output shows the validation results for different cluster sizes, detailing the objective function, energy, and gradient differences between calculated and reference values. It helps in identifying potential overfitting or areas where the force field needs improvement. ```text #=======================================================================# #| Target: cluster-02 Type: AbInitio_GMX Objective = 6.59279e-02 |# #| Difference Denominator Percent |# #| Physical Variable (Calc-Ref) RMS (Ref) Difference |# #=======================================================================# Energy (kJ/mol) 2.6852 8.9926 29.8605% Gradient (kJ/mol/A) 24.4491 120.0100 20.3725% ------------------------------------------------------------------------- #=======================================================================# #| Target: cluster-03 Type: AbInitio_GMX Objective = 6.86838e-02 |# #| Difference Denominator Percent |# #| Physical Variable (Calc-Ref) RMS (Ref) Difference |# #=======================================================================# Energy (kJ/mol) 4.1222 13.3676 30.8370% Gradient (kJ/mol/A) 24.1603 119.6514 20.1922% ------------------------------------------------------------------------- #=======================================================================# #| Target: cluster-04 Type: AbInitio_GMX Objective = 6.99336e-02 |# #| Difference Denominator Percent |# #| Physical Variable (Calc-Ref) RMS (Ref) Difference |# #=======================================================================# Energy (kJ/mol) 5.3337 17.0641 31.2567% Gradient (kJ/mol/A) 24.4117 121.2622 20.1313% ------------------------------------------------------------------------- #=======================================================================# #| Target: cluster-05 Type: AbInitio_GMX Objective = 6.83413e-02 |# #| Difference Denominator Percent |# #| Physical Variable (Calc-Ref) RMS (Ref) Difference |# #=======================================================================# Energy (kJ/mol) 6.4445 20.9275 30.7946% Gradient (kJ/mol/A) 24.2035 120.2407 20.1292% ------------------------------------------------------------------------- #=======================================================================# #| Target: cluster-06 Type: AbInitio_GMX Objective = 6.30676e-02 |# #| Difference Denominator Percent |# #| Physical Variable (Calc-Ref) RMS (Ref) Difference |# #=======================================================================# Energy (kJ/mol) 7.9083 27.3135 28.9539% Gradient (kJ/mol/A) 24.1990 119.0841 20.3209% ------------------------------------------------------------------------- #=======================================================================# #| Target: cluster-07 Type: AbInitio_GMX Objective = 7.23291e-02 |# #| Difference Denominator Percent |# #| Physical Variable (Calc-Ref) RMS (Ref) Difference |# #=======================================================================# Energy (kJ/mol) 9.0541 28.5018 31.7666% Gradient (kJ/mol/A) 24.5603 119.6730 20.5228% ------------------------------------------------------------------------- #=======================================================================# #| Target: cluster-08 Type: AbInitio_GMX Objective = 6.47534e-02 |# #| Difference Denominator Percent |# #| Physical Variable (Calc-Ref) RMS (Ref) Difference |# #=======================================================================# Energy (kJ/mol) 9.9105 33.9780 29.1676% Gradient (kJ/mol/A) 24.5318 118.7419 20.6598% ------------------------------------------------------------------------- #=======================================================================# #| Target: cluster-09 Type: AbInitio_GMX Objective = 6.31661e-02 |# ``` -------------------------------- ### Add Custom Python Module Location (PYTHONPATH) Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Append your custom module directory to the PYTHONPATH environment variable to ensure Python can find installed packages. ```bash export PYTHONPATH=$PYTHONPATH:/home/leeping/local/lib/python2.7 ``` -------------------------------- ### Prepare Simulation Directories and Copy Files Source: https://github.com/leeping/forcebalance/blob/master/studies/009_voelz_nspe/Nspe_2/About.txt This sequence of commands sets up the necessary directory structure and copies essential files (itp, gro, qdata, mdp, top) into the appropriate locations for running simulations and ForceBalance. ```bash cd .. mkdir forcefield cp Setup/molecule.itp forcefield mkdir -p simulations/2dscan cp Setup/all.gro !$ cp Setup/qdata.txt !$ mkdir simulations/2dscan/settings cp Setup/shot.mdp !$ cp Setup/topol.top !$ ``` -------------------------------- ### Create a Source Distribution Source: https://github.com/leeping/forcebalance/blob/master/README.txt Generates a distributable .tar.bz2 archive of the ForceBalance package. ```bash python setup.py sdist ``` -------------------------------- ### Get SHA256 Hash for Release Tarball Source: https://github.com/leeping/forcebalance/wiki/Home Command to get the SHA256 hash of a release tarball, used for updating the meta.yaml file in the conda-forge feedstock. ```bash curl -sL https://github.com/leeping/forcebalance/archive/vX.Y.Z.tar.gz | openssl sha256 ``` -------------------------------- ### Convert XYZ to GRO and QDATA with convert.py Source: https://github.com/leeping/forcebalance/blob/master/studies/009_voelz_nspe/Nspe_2/About.txt Execute the convert.py script to transform an XYZ file into ForceBalance-compatible all.gro and qdata.txt files. This script is part of a custom file format conversion library. ```bash ./convert.py < convert.in ``` -------------------------------- ### View Test Options Source: https://github.com/leeping/forcebalance/blob/master/src/tests/About.txt Display available command-line options for advanced test execution. ```bash python test -h ``` -------------------------------- ### Force Field Parameter Initialization Output Source: https://github.com/leeping/forcebalance/blob/master/doc/tutorial.txt This output section displays the initial indices, physical values, and names of parameters identified for optimization from the force field files. It helps in verifying the parameters ForceBalance will work with. ```text Reading force field from file: water.itp #=========================================================# #| Starting parameter indices, physical values and IDs |# #=========================================================# 0 [ 3.1537e-01 ] : VDWS:OW 1 [ 6.4852e-01 ] : VDWT:OW 2 [ 9.5720e-02 ] : BONDSB:HWOW 3 [ 5.0242e+05 ] : BONDSK:HWOW 4 [ 1.0452e+02 ] : ANGLESB:HWOWHW 5 [ 6.2802e+02 ] : ANGLESK:HWOWHW 6 [ 5.2000e-01 ] : COUL:SOL-2 COUL:SOL-3 7 [ -1.0400e+00 ] : COUL:SOL-4 8 [ 1.2800e-01 ] : VSITE3B:SOL-4 VSITE3A:SOL-4 ----------------------------------------------------------- ``` -------------------------------- ### Build ForceBalance from Source Source: https://github.com/leeping/forcebalance/blob/master/README.txt Compiles the ForceBalance package from its source code. ```bash python setup.py build ``` -------------------------------- ### Run ForceBalance Calculation Source: https://github.com/leeping/forcebalance/blob/master/studies/009_voelz_nspe/Nspe_2/About.txt Execute the main ForceBalance Python script with the specified options file to initiate the parameter optimization process. ```bash ForceBalance.py options.in ``` -------------------------------- ### Generate Documentation with Doxygen Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Command to run Doxygen from the doc directory to generate HTML and LaTeX documentation files. ```bash doxygen doxygen.cfg ``` -------------------------------- ### Test Case Class Inheritance Source: https://github.com/leeping/forcebalance/blob/master/src/tests/About.txt Example of how a test case class inherits from ForceBalanceTestCase and an abstract test class (TargetTests) to leverage shared test logic. ```python class TestAbInitio_GMX(ForceBalanceTestCase, TargetTests) ``` -------------------------------- ### Running ForceBalance Optimization Source: https://github.com/leeping/forcebalance/blob/master/doc/usage.txt The command to execute a ForceBalance optimization. Ensure the calculation is set up properly before running. ```bash ForceBalance.py input.in ``` -------------------------------- ### Generate AMBER Topology and Coordinate Files with Leap Source: https://github.com/leeping/forcebalance/blob/master/studies/009_voelz_nspe/Nspe_2/About.txt Run the Leap program with a specified input file to generate inpcrd and prmtop files, which are essential for AMBER force field simulations. ```bash tleap -f stage.leap ``` -------------------------------- ### Run ForceBalance for Validation Source: https://github.com/leeping/forcebalance/blob/master/doc/tutorial.txt Execute ForceBalance with a validation input file to evaluate the objective function using parameters from a previous optimization. Ensure the 'validate.in' file is correctly configured with the 'single' job type and includes QM energies and forces for various cluster sizes. ```bash ForceBalance.py validate.in ``` -------------------------------- ### Create Git Tag for Versioning Source: https://github.com/leeping/forcebalance/blob/master/doc/roadmap.txt Use this command to create a new version tag in Git. Ensure to replace 'v1.2.1' with your desired version number and provide a descriptive message. ```bash git tag -a v1.2.1 -m "version 1.2.1" git push --tags ``` -------------------------------- ### Generate Mol2 File with Babel and Antechamber Source: https://github.com/leeping/forcebalance/blob/master/studies/009_voelz_nspe/Nspe_2/About.txt Convert an XYZ file to PDB format using Babel, then process the PDB with Antechamber to generate a mol2 file. This is a prerequisite for creating force field files. ```bash head -30 all.xyz > molecule.xyz babel -ixyz molecule.xyz -opdb molecule.pdb antechamber -i molecule.pdb -fi pdb -o molecule.mol2 -fo mol2 -c bcc -pf y ``` -------------------------------- ### Load AMBER-FB15 Force Field in OpenMM Source: https://github.com/leeping/forcebalance/blob/master/Products/AMBER-FB15/About.txt Use this command to create a ForceField object in OpenMM when amberfb15.xml and tip3pfb.xml are in the current directory. ```python forcefield = ForceField('amberfb15.xml', 'tip3pfb.xml') ``` -------------------------------- ### Checkout ForceBalance from Subversion Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Downloads the latest revision of the ForceBalance source code directly from the SimTK Subversion repository. This is an alternative to downloading a tarball. ```bash svn checkout https://simtk.org/svn/forcebalance ``` -------------------------------- ### Load AMBER-FB15 Force Field in AMBER tleap Source: https://github.com/leeping/forcebalance/blob/master/Products/AMBER-FB15/About.txt Source these files in tleap to load the AMBER-FB15 force field and water parameters. ```bash source leaprc.protein.fb15 source leaprc.water.fb3 ``` -------------------------------- ### Standard Test Module Imports Source: https://github.com/leeping/forcebalance/blob/master/src/tests/About.txt Essential imports for creating ForceBalance unit test modules. These should be included at the beginning of each test file. ```python from __init__ import ForceBalanceTestCase import unittest import forcebalance ``` -------------------------------- ### Minimal ForceBalance Input File Source: https://github.com/leeping/forcebalance/blob/master/doc/usage.txt A basic input file for a ForceBalance job, defining global options and target sections. Global options include job type and force field file, while target options specify the target name and type. ```text $options jobtype newton forcefield water.itp $end $target name cluster-02 type abinitio_gmx $end $target name cluster-03 type abinitio_gmx $end ``` -------------------------------- ### Convert XYZ to PDB and Generate Mol2 with Antechamber Source: https://github.com/leeping/forcebalance/blob/master/studies/009_voelz_nspe/Nspe_2/About_VAV.txt Converts an XYZ file to PDB format and then uses Antechamber to generate a mol2 file from the PDB. This is used to prepare molecular structure files. ```bash cp structures/xyz/min.omega.0.chi1.240.phi1.270.xyz molecule.xyz babel -ixyz molecule.xyz -opdb molecule.pdb antechamber -i molecule.pdb -fi pdb -o molecule.mol2 -fo mol2 -c bcc -pf y ``` -------------------------------- ### Specify Optimizable Parameters in Force Field File Source: https://github.com/leeping/forcebalance/blob/master/doc/tutorial.txt Mark parameters for optimization within a force field file (e.g., water.itp) by appending a comment with 'PRM' followed by parameter field indices. This tells ForceBalance which values to adjust. ```text OW 8 15.99940 0.000 A 3.15365e-01 6.48520e-01 ; PRM 5 6 ``` -------------------------------- ### ForceBalance Optimization Output Source: https://github.com/leeping/forcebalance/blob/master/doc/tutorial.txt This output details the progress of a ForceBalance optimization run, including target information, physical variable differences, objective function breakdown, and step-by-step convergence metrics. It is useful for understanding the optimization process and identifying areas of improvement. ```text #=======================================================================# #| Target: cluster-06 Type: AbInitio_GMX Objective = 6.30676e-02 |# #| Difference Denominator Percent |# #| Physical Variable (Calc-Ref) RMS (Ref) Difference |# #=======================================================================# Energy (kJ/mol) 7.9083 27.3135 28.9539% Gradient (kJ/mol/A) 24.1991 119.0841 20.3210% ------------------------------------------------------------------------- #=======================================================================# #| Target: cluster-12 Type: AbInitio_GMX Objective = 5.89806e-02 |# #| Difference Denominator Percent |# #| Physical Variable (Calc-Ref) RMS (Ref) Difference |# #=======================================================================# Energy (kJ/mol) 12.9053 47.3455 27.2578% Gradient (kJ/mol/A) 24.3021 118.0240 20.5908% ------------------------------------------------------------------------- #===================================================================================# #| Objective Function Breakdown |# #| Target Name Residual x Weight = Contribution (Current-Prev) |# #===================================================================================# cluster-06 0.06307 0.500 3.15338e-02 ( -4.544e-07 ) cluster-12 0.05898 0.500 2.94903e-02 ( -7.454e-06 ) Regularization 0.00170 1.000 1.70115e-03 ( +7.704e-06 ) Total 6.27252e-02 ( -2.045e-07 ) ------------------------------------------------------------------------------------- Step |k| |dk| |grad| -=X2=- Delta(X2) StepQual 5 4.124e-01 2.498e-03 2.130e-05 6.27252e-02 2.045e-07 1.029 Convergence criterion reached for gradient norm (1.00e-04) @========================================================@ @| Final objective function value |@ @| Full: 6.272524e-02 Un-penalized: 6.102410e-02 |@ @========================================================@ ``` ```text #========================================================# #| Final optimization parameters: |# #| Paste to input file to restart |# #========================================================# read_mvals 0 [ 3.3161e-02 ] : VDWS:OW 1 [ 4.3311e-02 ] : VDWT:OW 2 [ 5.5070e-03 ] : BONDSB:HWOW 3 [ -4.5933e-02 ] : BONDSK:HWOW 4 [ 1.5497e-02 ] : ANGLESB:HWOWHW 5 [ -3.7655e-01 ] : ANGLESK:HWOWHW 6 [ 2.4929e-03 ] : COUL:SOL-2 COUL:SOL-3 7 [ 1.1874e-02 ] : COUL:SOL-4 8 [ 1.5108e-01 ] : VSITE3B:SOL-4 VSITE3A:SOL-4 /read_mvals #========================================================# #| Final physical parameters: |# #========================================================# 0 [ 3.1712e-01 ] : VDWS:OW 1 [ 7.5589e-01 ] : VDWT:OW 2 [ 9.6011e-02 ] : BONDSB:HWOW 3 [ 4.5935e+05 ] : BONDSK:HWOW 4 [ 1.0541e+02 ] : ANGLESB:HWOWHW 5 [ 3.9986e+02 ] : ANGLESK:HWOWHW 6 [ 5.2249e-01 ] : COUL:SOL-2 COUL:SOL-3 7 [ -1.0281e+00 ] : COUL:SOL-4 8 [ 1.3599e-01 ] : VSITE3B:SOL-4 VSITE3A:SOL-4 ---------------------------------------------------------- ``` ```text #========================================================# #| Congratulations, ForceBalance has finished |# #| Give yourself a pat on the back! |# #========================================================# ``` -------------------------------- ### Quantum Data File Format Source: https://github.com/leeping/forcebalance/blob/master/doc/usage.txt Specifies the format for quantum data files, including job information, coordinates, energy, and forces. Ensure consistency between coordinate trajectory and quantum data files. ```text @verbatim JOB 0 COORDS x1 y1 z1 x2 y2 z2 ... (floating point numbers in Angstrom) ENERGY (floating point number in Hartree) FORCES fx1 fy1 fz1 ... (floating point numbers in Hartree/bohr - this is a misnomer because they are actually gradients, which differ by a sign from the forces.) JOB 1 ... @endverbatim ``` -------------------------------- ### Electrostatic Potential Data File Format Source: https://github.com/leeping/forcebalance/blob/master/doc/usage.txt Defines the format for quantum data files when evaluating electrostatic potentials. Includes coordinates, energy, forces, and electrostatic potential specific data. ```text @verbatim JOB 0 COORDS x1 y1 z1 x2 y2 z2 ... ENERGY e FORCES fx1 fy1 fz1 ... ESPXYZ ex1 ey1 ez1 ex2 ey2 ez2 ... ESPVAL ev1 ev2 ev3 .. @endverbatim ``` -------------------------------- ### Split Topology File into ITP and TOP with awk Source: https://github.com/leeping/forcebalance/blob/master/studies/009_voelz_nspe/Nspe_2/About.txt Use awk commands to split a condensed Gromacs topology file into separate .itp and .top files. The first awk command extracts parameters before the 'system' keyword, and the second extracts from 'system' to 'neverever'. ```bash awk '/system/ {exit} {print}' LIG_GMX_bytype.top > molecule.itp awk '/system/,/neverever/' LIG_GMX_bytype.top > topol.top ``` -------------------------------- ### Standard Test Module Execution Source: https://github.com/leeping/forcebalance/blob/master/src/tests/About.txt Enables test modules to be run as standalone scripts using the default unittest runner. ```python if __name__ == '__main__': unittest.main() ``` -------------------------------- ### Update Conda-Forge Feedstock Repository Source: https://github.com/leeping/forcebalance/wiki/Home Commands to update a personal fork of the forcebalance-feedstock repository. Replace YOURUSERNAME with your GitHub username. ```bash git pull --set-upstream git@github.com:conda-forge/forcebalance-feedstock.git git push --set-upstream git@github.com:YOURUSERNAME/forcebalance-feedstock.git ``` -------------------------------- ### Condense Interactions by Atom Type with Condense_Interactions.py Source: https://github.com/leeping/forcebalance/blob/master/studies/009_voelz_nspe/Nspe_2/About.txt This script condenses interaction parameters in a Gromacs topology file, grouping them by atom type rather than individual atoms. This can simplify the topology file for certain analyses. ```bash ~/scripts/forcebalance/bin/Extras/Condense_Interactions.py LIG_GMX.top > LIG_GMX_bytype.top ``` -------------------------------- ### Checkout Specific Git Commit for ForceBalance Source: https://github.com/leeping/forcebalance/blob/master/Products/AMBER-FB15/About.txt Revert to this specific Git commit to exactly reproduce older results if using a newer version of ForceBalance. ```bash git checkout 2fb85e65e6fd508f37f1265b0aca7f0090fbe7c8 ``` -------------------------------- ### Extract GROMACS-X2 Tarball Source: https://github.com/leeping/forcebalance/blob/master/doc/installation.txt Extract the downloaded GROMACS-X2 tarball using this command. Replace '[version]' with the actual version number. ```bash tar xvjf gromacs-[version]-x2.tar.bz2 ```