Note 1: Please read the setup guide for the installation of ForceBalance and other packages.
Note 2: The fitting results are posted as release packages in this repository. You can find release_XX.tar.gz which contains fitting results and all codes used in the fitting procedure for the release.
Fitting valence parameters to QM data can be performed in four steps.
(1) QM data generation and submission. Quantum chemical calculations, which are the most expensive part of the fitting procedure, are performed using the MolSSI QCFractal distributed quantum chemistry engine.
(2) Pulling QM data from QCArchive and processing into ForceBalance native formats. The data is stored as DataSet objects on the public MolSSI QCArchive server and can be pulled using the qcportal Python API. In this step, we pull the data, filter and format them into ForceBalance fitting targets. Typical filters include “toolkit capability”, “topology consistency”, and “avoid hydrogen bonds”.
(3) Optimization of valence parameters by fitting to QM data. The main fitting procedure is carried out by the open-source software package ForceBalance, which is maintained by the Wang research group. In this step we prepare the input files for the ForceBalance command line application, then run ForceBalance to carry out the optimization.
(4) Analysis of the optimized force field. After the fitting is finished, the output file and temporary folder contain many details; to get insights into these, we perform several analyses that aggregate the fitting data and produce various plots and tables.
Quantum chemical calculations are performed on a distributed set of high-performance computing clusters using the MolSSI QCFractal distributed quantum chemistry engine, and stored as DataSet objects on the public MolSSI QCArchive server.
For the release-1 "Parsley" parameter optimization, two sets of molecules were used, and each leads to three types of QM data being generated: 1) Optimized geometries; 2) Vibrational frequencies; 3) Torsion profiles. Thus there are 6 QM data sets in total.
Table 1. Collection types and names of datasets of 6 QM data sets specified on QCArchive server.
| Collection type | Name for "Roche set" | Name for "Coverage set" | |
|---|---|---|---|
| Optimized geometries | OptimizationDataset | OpenFF Optimization Set 1 | SMIRNOFF Coverage Set 1 |
| Vibrational frequencies | Dataset | OpenFF Optimization Set 1 | SMIRNOFF Coverage Set 1 |
| Torsion profiles | TorsionDriveDataset | OpenFF Optimization Set 1 | SMIRNOFF Coverage Set 1 |
The blog post provides a nice overview of the background behind the selection and generation of datasets. For details about how to generate and submit data, please check https://github.com/openforcefield/qca-dataset-submission.
2. Pulling QM data from QCArchive and processing into ForceBalance native formats for parameter fitting.
Note: The result of this step was aggregated into the fb-fit/targets/ folder of the release package. Thus if you want to reproduce the fitting without changing the targets, please skip to the next step.
The results of quantum chemical calculations are stored as DataSet objects on the public MolSSI QCArchive and can be pulled from the server.
To list the available QM data sets on QCArchive server, run the following in a Jupyter notebook or Python console:
import qcportal as ptl
client = ptl.FractalClient('https://api.qcarchive.molssi.org:443/')
client.list_collections()
The list of all available collections currently on the server will be printed to the console.
Open a terminal and go to an empty folder. From now on, all related files will be placed into this folder.
-
Clone the following repository for a set of scripts to convert the QCArchive data:
git clone https://github.com/openforcefield/openforcefield-forcebalance.git -
Create a new folder to carry out the remaining steps:
mkdir make-target cd make-target -
To ensure the targets generated are compatible with the toolkit using this force field file, we copy over the force field
.offxmlfile that is going to be used in parameter fitting. One such file can be found in the release packagefb-fit/forcefield/param_valence.offxml. You can also download the input force field file we used in the release-1 fitting:wget https://github.com/openforcefield/openforcefield-forcebalance/releases/download/v1.0.0-RC2/input_ff.offxml
In release-1 we used two OptimizationDatasets, namely “OpenFF Optimization Set 1” and “SMIRNOFF Coverage Set 1”. To pull “OpenFF Optimization Set 1” and generate a list of ForceBalance targets:
mkdir optgeo-opt-set1; cd optgeo-opt-set1
python ~/codes/openforcefield-forcebalance/optimized_geo/make_fb_optgeo_target.py “OpenFF Optimization Set 1” -t ../input_ff.offxml | tee run.log
This will 1) pull the data set from QCArchive; 2) filter the data to exclude cases where the bonding pattern changes during QM optimization and cases where the data introduces errors for the openforcefield toolkit. The molecules which are filtered out can be found in error_mol2s in the target folder generated. and 3) format the data into ForceBalance targets.
The progress will be printed on the screen and saved in the log file run.log. The resulting files and folders are saved in the targets/ folder. Each subfolder is a ForceBalance target that we will use later in the fitting. A file named “targets/target.XXXX.in” is also generated that will be used when preparing the ForceBalance input file.
Repeat the same commands for the “Coverage set”:
cd ..; mkdir optgeo-coverage-set1; cd optgeo-coverage-set1
python ../../openforcefield-forcebalance/optimized_geo/make_fb_optgeo_target.py “SMIRNOFF Coverage Set 1” -t ../input_ff.offxml | tee make_target.log
Notice that the only argument changed is the name of the dataset “SMIRNOFF Coverage Set 1”.
To pull the hessian data from the DataSet “OpenFF Optimization Set 1” and generate vibrational frequency fitting targets:
cd ..; mkdir vibfrq-opt-set1; cd vibfrq-opt-set1
python ../../openforcefield-forcebalance/vib_freq_target/make_vib_frq_target.py “OpenFF Optimization Set 1” -t ../input_ff.offxml | tee run.log
This will 1) download Hessian data for each optimized geometry; 2) pick the lowest-energy conformer of each molecule; 3) apply the toolkit-compatibility and topology-check filters; 4) perform normal mode analysis to get the vibrational frequencies; and 5) write the data into targets/ folder for ForceBalance.
To repeat the process for “SMIRNOFF Coverage Set 1”:
cd ..; mkdir vibfrq-coverage-set1; cd vibfrq-coverage-set1
python ../../openforcefield-forcebalance/vib_freq_target/make_vib_frq_target.py “SMIRNOFF Coverage Set 1” -t ../input_ff.offxml | tee runmake_target.log
To generate the fitting targets for a TorsionDriveDataset “OpenFF Optimization Set 1”:
cd ..; mkdir td-opt-set1; cd td-opt-set1
python ../../openforcefield-forcebalance/torsion_target/make_torsion_target_new.py “OpenFF
Optimization Set 1” -t ../input_ff.offxml | tee run.log
This script pulls torsion scan trajectories from the server, filters out trajectories that contain any frame with hydrogen bonds, and formats into ForceBalance torsion profiles targets, while saving the useful metadata about the torsiondrive records as metadata.json in each target folder.
Repeating the process for “SMIRNOFF Coverage Set 1”:
cd ..;mkdir td-coverage-set1;cd td-coverage-set1
python ../../openforcefield-forcebalance/torsion_target/make_torsion_target_new.py “SMIRNOFF Coverage Set 1” -t ../input_ff.offxml | tee run.log
ForceBalance is a free software designed for carrying out force field optimizations using a systematic and reproducible procedure.
Note: The result of steps 3.1 and 3.2 are provided in the release package.
3.1. Create fb-fit in the same location as the make-target/ folder from last step. We are going to run ForceBalance in here:
mkdir fb-fit
cd fb-fit
Notice that all needed files are already provided in the release package under fb-fit/ folder. The following steps can be used to re-create these files.
The directory named forcefield contains the force field files that you are optimizing. Parameters to be optimized are specified by parameterize tags.
For example, if we want to fit the force constant and the equilibrium bond length of the bond term with string ID b1, the attribute parameterize=”k,length” should be added as shown below.
<Bond smirks="[#6X4:1]-[#6X4:2]" length="1.526 * angstrom" k="620.0 * angstrom**-2 * mole**-1 * kilocalorie" id="b1" parameterize="k,length"/>
You can get the directory directly from the release package and use it for the calculation, or you can manually modify the input force field files as needed. When doing so, it is preferred to use the openforcefield toolkit for the modification of the file.
The directory named targets contains reference data sets as well as input files for simulating that data using the force field.
Each subdirectory in targets corresponds to a single "ForceBalance target" or data set, and its contents depends on the specific target type.
Since the targets from the previous step can be directly used in ForceBalance fitting, we can copy and merge all the prepared files into one folder.
cp -r ../make-target/*/targets .
The ForceBalance input file contains a "global options" section, starting with $options, that specifies global properties of the optimization.
There are also "target options" section(s), starting with $target, which specify the settings of one or more ForceBalance targets.
An example input file is provided as optimize.in in the release package under the fb-fit/ folder.
Global options:
jobtype, specifies the calculation type. To run force field optimization, set jobtype to optimize. To run single-point calculation, set jobtype to single.
The provided optimize.in contains two global options wq_port, and asynchronous that specify the use of Work Queue for distributed target evaluations.
Please refer to the setup guide if you are using Work Queue for the first time.
If you intend to run small optimization jobs on your local machine, please remove these two options.
The settings for fitting targets are given as $target blocks, one for each target.
The provided optimize.in contains a long list of such blocks.
To reproduce these input blocks, you can clean upall of them from optimize.in, then append the updated input options by:
cat targets/target*.in >> optimize.in
The ForceBalance optimizer is executed on the command line as:
ForceBalance optimize.in
The executable is intended to be run in the foreground, allowing you to view outputs in real time.
The output will be printed on the screen and also saved in the output file optimize.out.
Although it is possible to run in the background, the recommended workflow is to run ForceBalance in an open terminal window or a virtual console, e.g. provided by the GNU Screen or tmux software packages.
All fitting related temporary files containing the details are saved in the directory optimize.tmp/.
This folder is too large to be included in the release package.
After the fitting is finished, the resulting forcefield file is saved in the result/ folder.
Several scripts for visualization of fitting results can be found in analysis_scripts/ directory. They help to get insights on ForceBalance output data.
Note: The results of this step is provided in the release package in the analysis/ folder.
4.1 Create a new folder for saving the analysis results, in the same location as the fb-fit/ folder.
mkdir analysis
cd analysis
In this step, we will read the ForceBalance output file to generate bar plots of parameter changes, with green and red colors indicating an increase/decrease in the parameter value respectively.
python ../openforcefield-forcebalance/analysis_scripts/visualize_fb_parameters.py ../fb-fit/optimize.out -x ../fb-fit/forcefield/param_valence.offxml
The result of this script is saved in a folder param_change/, with each type of parameter in one pdf file.
The all.pdf combines the parameter changes for all parameter types into a single file.
To visualize the effect of fitting on optimized geometries, we run a script to read the QM and MM internal coordinate values for every molecule from the optimize.tmp folder.
The script aggregates the internal coordinate values according to their matching SMIRKS patterns from the force field file and draws scatter plots with initial and final values of the equilibrium parameter as vertical lines.
Each dot corresponds to one internal coordinate in an optimized structure.
python ../openforcefield-forcebalance/analysis_scripts/plot_optgeo_each_smirks.py -x ../fb-fit/forcefield/param_valence.offxml --new_xml../fb-fit/result/optimize/param_valence.offxml -f ../fb-fit/optimize.tmp -t ../fb-fit/targets-j ../fb-fit/smirnoff_parameter_assignments.json
This script will generate a folder optgeo_scatter_plots/, that contains subfolders like Bonds/.
The PDF files in each folder correspond to the SMIRKS id, such as b1.pdf.
This script will also save a pickle file optgeo_analysis_data.p on disk for quickly generating the plots without re-reading the data from optimize.tmp.
To visualize the effect of fitting on vibrational frequencies, a script was implemented to plot the bar chart of RMSD of QM and MM vibrational frequencies from the zeroth optimization cycle (before any parameter changes) and the final optimization cycle.
python ../openforcefield-forcebalance/analysis_scripts/plot_vibfreq_rmsd.py -f ../fb-fit/optimize.tmp
This script will generate a folder vibfreq_targets_plots/ that contains two files, the vib_freq_rmsd.pdf and vib_freq_maxdiff.pdf.
A pickle file vibfreq_plot_data.pickle is also saved for re-using the loaded data when making new plots.
We use a script to load data from optimize.tmp/ directory and generate QM and MM energy profiles as a function of the the torsion angle, including the MM energies from both the zeroth cycle (before any parameter changes) and the final optimization cycle for comparison.
A table of metadata is also included in each plot.
Plot files are organized into subfolders by the ID of the matching SMIRKS pattern.
python ../openforcefield-forcebalance/analysis_scripts/plot_td_energies.py -f ../fb-fit/optimize.tmp -t ../fb-fit/targets
This script will generate a folder td_targets_plots/ that contains subfolders corresponding to each SMIRKs torsion term.
Each PDF file has the same name as the corresponding torsion profile target such as td_OpenFF_Group1_Torsions_193_C11H18N2.pdf.
The log of running all above analysis scripts is saved in the release package as analysis/run_analysis.log.
Congratulations! Now you have completed the full fitting tutorial. Please make sure you read the blog post for the theory and ideas behind this optimization.
For questions about this tutorial, details on the fitting releases, or ForceBalance, please contact Hyesu Jang, Yudong Qiu, or Lee-Ping Wang. We are also planning to rewrite the ForceBalance documentation with updated instructions and more detailed explanations.