### Install Bartender Binary (Linux) Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Download and configure the pre-built binary distribution. Ensure xtb is available in your PATH. This method does not require compilation. ```bash # 1. Download the latest release tarball from GitHub and uncompress it tar -xzf Bartender_2024_itps.tar.gz -C /home/user/bartender # 2. Set the required environment variables (bash example) echo "export BTROOT=/home/user/bartender" >> ~/.bashrc echo "source \$BTROOT/bartender_config.sh" >> ~/.bashrc source ~/.bashrc # bartender_config.sh sets up xtb paths, OMP threads, and library paths: # export XTBHOME=$BTROOT/xtb-6.6.0 # export OMP_MAX_ACTIVE_LEVELS=1 # export OMP_STACKSIZE=2G # export OMP_NUM_THREADS=4,1 # set to match your machine # export MKL_NUM_THREADS=4 # same # ulimit -s unlimited # source $XTBHOME/share/xtb/config_env.bash # export PATH=$BTROOT:$PATH # export LD_LIBRARY_PATH=$BTROOT/xdrlib/lib:$LD_LIBRARY_PATH # 3. Verify installation bartender -help ``` -------------------------------- ### PDB File Format Example Source: https://github.com/martini-force-field-initiative/bartender/wiki/example This is an example of the Beads.pdb file generated by Bartender. It follows the PDB format and contains atom coordinates. The 'residue number' column indicates bead membership, and the temperature-factor field can be used for visualization by bead. ```pdb REMARK WRITTEN WITH GOCHEM :-) ATOM 0 O UNK 11 -3.771 -8.617 15.375 0.00 90.91 O ATOM 0 C UNK 11 -3.844 -8.496 13.959 0.00 90.91 C ATOM 0 C UNK 10 -3.684 -7.020 13.540 0.00 81.82 C ATOM 0 O UNK 10 -3.757 -6.878 12.113 0.00 81.82 O ATOM 0 C UNK 10 -3.653 -5.711 11.398 0.00 81.82 C ATOM 0 O UNK 10 -3.475 -4.635 12.020 0.00 81.82 O ATOM 0 C UNK 9 -3.743 -5.721 9.977 0.00 72.73 C ATOM 0 C UNK 9 -3.942 -6.931 9.269 0.00 63.64 C ATOM 0 C UNK 7 -4.031 -6.946 7.866 0.00 54.55 C ATOM 0 C UNK 8 -3.924 -5.750 7.114 0.00 59.09 C ATOM 0 C UNK 8 -3.725 -4.544 7.825 0.00 63.64 C ATOM 0 C UNK 9 -3.636 -4.525 9.224 0.00 68.18 C ATOM 0 C UNK 6 -4.014 -5.757 5.694 0.00 45.45 C ATOM 0 O UNK 6 -4.192 -6.830 5.068 0.00 45.45 O ATOM 0 O UNK 6 -3.908 -4.585 4.996 0.00 45.45 O ATOM 0 C UNK 6 -3.977 -4.415 3.578 0.00 45.45 C ATOM 0 C UNK 5 -3.811 -2.928 3.216 0.00 36.36 C ATOM 0 O UNK 5 -3.886 -2.790 1.791 0.00 36.36 O ATOM 0 C UNK 5 -3.646 -1.629 1.122 0.00 36.36 C ATOM 0 O UNK 5 -4.649 -0.988 0.730 0.00 36.36 O ATOM 0 C UNK 4 -2.320 -1.216 0.818 0.00 22.73 C ATOM 0 C UNK 4 -1.228 -2.092 1.022 0.00 27.27 C ATOM 0 C UNK 4 0.088 -1.695 0.727 0.00 18.18 C ATOM 0 C UNK 2 0.363 -0.405 0.216 0.00 9.09 C ATOM 0 C UNK 3 -0.732 0.469 0.013 0.00 13.64 C ATOM 0 C UNK 3 -2.049 0.074 0.308 0.00 18.18 C ATOM 0 C UNK 1 1.692 0.004 -0.086 0.00 0.00 C ATOM 0 O UNK 1 1.964 1.237 -0.577 0.00 0.00 O ATOM 0 O UNK 1 2.678 -0.749 0.082 0.00 0.00 O ATOM 0 H UNK 11 -3.710 -9.545 15.614 0.00 90.91 H ATOM 0 H UNK 11 -2.984 -9.049 13.582 0.00 90.91 H ATOM 0 H UNK 11 -4.856 -8.812 13.700 0.00 90.91 H ATOM 0 H UNK 10 -4.544 -6.473 13.926 0.00 81.82 H ATOM 0 H UNK 10 -2.674 -6.709 13.805 0.00 81.82 H ATOM 0 H UNK 9 -4.028 -7.869 9.818 0.00 72.73 H ATOM 0 H UNK 7 -4.183 -7.896 7.356 0.00 54.55 H ATOM 0 H UNK 8 -3.637 -3.603 7.281 0.00 63.64 H ATOM 0 H UNK 9 -3.484 -3.575 9.737 0.00 72.73 H ATOM 0 H UNK 6 -3.116 -4.955 3.182 0.00 45.45 H ATOM 0 H UNK 6 -4.987 -4.717 3.300 0.00 45.45 H ATOM 0 H UNK 5 -4.670 -2.385 3.611 0.00 36.36 H ATOM 0 H UNK 5 -2.800 -2.624 3.488 0.00 36.36 H ATOM 0 H UNK 4 -1.406 -3.094 1.414 0.00 27.27 H ATOM 0 H UNK 2 0.906 -2.396 0.898 0.00 9.09 H ATOM 0 H UNK 2 -0.557 1.470 -0.380 0.00 9.09 H ATOM 0 H UNK 3 -2.869 0.772 0.141 0.00 18.18 H TER END ``` -------------------------------- ### Complete Workflow Example: PET Dimer - Initial Bartender Run Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Runs Bartender with a short trajectory for testing purposes. This step generates intermediate files for verification and analysis. ```bash # 2. Run Bartender with a short trajectory for testing bartender -time 100 -v 2 ligand.xyz bartender.inp ``` -------------------------------- ### Get Bartender Help Source: https://github.com/martini-force-field-initiative/bartender/blob/master/README.md Use this command to display all available flags for Bartender and their usage instructions. ```bash bartender -help ``` -------------------------------- ### Compile Bartender from Source (No XTC) Source: https://github.com/martini-force-field-initiative/bartender/wiki/Home Use this command to compile Bartender from source if XTC trajectory format support is not required. Assumes Go toolchain is installed. ```bash go install github.com/Martini-Force-Field-Initiative/Bartender ``` -------------------------------- ### Complete Workflow Example: PET Dimer - Merge with Reference Topology Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Merges the Bartender-generated parameters with a reference topology to create the final `.itp` file for simulation. This is the final step in assembling the complete topology. ```bash # 6. Merge with reference topology for final itp python utils/produce_bartender_sm3_itps.py \ -l list_mol -r ref_itps/ -b bartender_output/ ``` -------------------------------- ### Compile Bartender from Source (With XTC) Source: https://github.com/martini-force-field-initiative/bartender/wiki/Home Compile Bartender from source with XTC trajectory format support. Requires prior installation of xdrlibrary and setting relevant shell variables. ```bash go build -tags "xtc" ``` -------------------------------- ### Run Replica-Exchange MD with Explicit Replica Count Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Launches a temperature replica-exchange simulation with a specified number of replicas and a custom exchange frequency. This provides more control over the simulation setup. ```bash # Explicit replica count with custom exchange frequency bartender -re -replicas 10 -exfreq 5 -time 5000 ligand.xyz bartender.inp ``` -------------------------------- ### Complete Workflow Example: PET Dimer - Production Run Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Executes Bartender for a production run, typically 10 ns, saving the trajectory. This command is used for generating the final parameters and trajectory. ```bash # 4. Production run (default 10 ns, save trajectory) bartender -time 10000 -dcdSave pet_traj.dcd ligand.xyz bartender.inp ``` -------------------------------- ### Define Bonds, Angles, Dihedrals, and Impropers Source: https://github.com/martini-force-field-initiative/bartender/blob/master/README.md Example of how to list bonded terms in the respective sections of the input file. Each line specifies the beads involved in the interaction. ```plaintext BONDS 1,2 2,3 ANGLES 1,4,5 1,4,6 DIHEDRALS 1,2,4,5 IMPROPERS 3,2,1,4 ``` -------------------------------- ### Complete Workflow Example: PET Dimer - Re-fit from Trajectory Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Re-fits parameters using a previously saved trajectory without performing new MD simulations. This is useful for refining parameters based on existing trajectory data. ```bash # 5. Re-fit from saved trajectory if needed (no new MD) bartender -owntraj pet_traj.dcd ligand.xyz bartender.inp ``` -------------------------------- ### Bartender Input File Structure Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Defines the atom-to-bead mapping and bonded terms for Bartender. Sections must appear in the specified order: BEADS, VSITES, BONDS, ANGLES, DIHEDRALS, IMPROPERS. Comments start with '#'. ```inp # bartender.inp for 2-unit PET (polyethylene terephthalate), 46 atoms, 11 beads # # BEADS section: BeadNumber atom1,atom2,...,atomN # Split atoms use BeadNumber atomL/M (assigns 1/M of atomL to this bead) BEADS 1 27,28,29 2 44,45,23/2,25/2,24 3 26,21/2,25/2,46 4 22,23/2,43,21/2 5 42,41,20,18,19,17 6 15,40,13,16,39,14 7 10/2,9,36,8/2 8 10/2,11,12/2,37 9 35,7,12/2,38,8/2 10 33,6,34,4,5,3 11 2,30,31,1,32 # VSITES section: VsiteNumber Bead1,...,BeadN, Param1,...,ParamM, GromacsFunctionNumber # (empty — no virtual sites in this molecule) VSITES # BONDS: pairs of bead indices BONDS 1,2 2,3 2,4 3,4 3,5 5,6 6,7 7,8 7,9 8,9 9,10 10,11 # ANGLES: triplets of bead indices ANGLES 1,2,3 4,3,5 3,5,6 5,6,7 6,7,8 5,6,11 7,9,10 9,10,11 4,6,7 1,6,11 # DIHEDRALS: quadruplets of bead indices DIHEDRALS 7,9,10,11 1,5,6,11 # IMPROPERS: quadruplets of bead indices IMPROPERS 3,5,6,7 2,3,4,1 2,4,3,5 7,8,9,6 9,7,8,10 ``` -------------------------------- ### Auto-generate Bartender Input from Topology Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt This Python script converts a GROMACS index file (.ndx) and a coarse-grained topology (.itp) into a Bartender input file (.inp). It's useful when starting from existing CG models. ```bash # General usage python utils/write_bartender_inp.py \ --ndx molecule_oplsaaTOcg.ndx \ --itp molecule_cog.itp \ --out molecule_bartender.inp # Benzene example python utils/write_bartender_inp.py \ --ndx utils/inputs/BENZ_oplsaaTOcg_cgbuilder.ndx \ --itp utils/inputs/BENZ_cog.itp \ --out BENZ_bartender.inp ``` -------------------------------- ### Validate Dihedral Parameters using Sommelier Mode Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Tests newly generated dihedral parameters in a short classical MD simulation using GROMACS before committing to a full CG simulation. Requires GROMACS and `insane` to be installed. ```bash # Validate dihedral parameters using an existing GROMACS topology bartender -sommelier molecule.top ligand.xyz bartender.inp ``` -------------------------------- ### Compile Bartender from Source (No XTC Support) Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Compile Bartender from source using Go. Requires Go 1.22+ and xtb to be in your PATH. ```bash # Requires Go 1.22+ and xtb in PATH go install www.github.com/rmera/bartender@latest ``` -------------------------------- ### Run Replica-Exchange MD with Solvent and Charge Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Launches a temperature replica-exchange simulation including solvent and charge specifications. This is useful for simulating systems with explicit solvent or net charge. ```bash # With solvent and charge bartender -re -replicas 8 -charge -1 -solvent h2o -time 10000 ligand.xyz bartender.inp ``` -------------------------------- ### Bartender Input File (bartender.inp) Source: https://github.com/martini-force-field-initiative/bartender/wiki/example This file defines the topology for Bartender, including bead definitions, bonds, angles, dihedrals, and impropers. Ensure the order of sections is correct (BEADS, VSITES, BONDS, ANGLES, DIHEDRALS, IMPROPRS). ```text BEADS 1 27,28,29 2 44,45,23/2,25/2,24 3 26,21/2,25/2,46 4 22,23/2,43,21/2 5 42,41,20,18,19,17 6 15,40,13,16,39,14 7 10/2,9,36,8/2 8 10/2,11,12/2,37 9 35,7,12/2,38,8/2 10 33,6,34,4,5,3 11 2,30,31,1,32 BONDS 1,2 2,3 2,4 3,4 3,5 5,6 6,7 7,8 7,9 8,9 9,10 10,11 ANGLES 1,2,3 4,3,5 3,5,6 5,6,7 6,7,8 5,6,11 7,9,10 9,10,11 4,6,7 1,6,11 DIHEDRALS 7,9,10,11 1,5,6,11 IMPROPERS 3,5,6,7 2,3,4,1 2,4,3,5 7,8,9,6 9,7,8,10 ``` -------------------------------- ### Bartender Input File Structure Source: https://github.com/martini-force-field-initiative/bartender/wiki/Home This is a sample Bartender input file demonstrating the structure for defining beads, virtual sites, and bonded terms. Ensure all lines have information or are comments, and avoid empty lines. ```text #Lines starting with "#" are comments. Only "full line" comments are allowed! #note that you can assign half (or less) of an atom to a bead. #Just divide it by the number you want. Note that all the #atom and bead numbers are 1-based BEADS 1 8,9,10,18,19,20,21 2 6/2,11,20 3 6/2,7,17 #you can add comment lines anywhere 4 16,5,22,1,12 5 15,4,3/2,14/2 6 13,2,3/2,14/2 #The virtual sites section is similar to the #BEADS section, except for the last field #which is the Gromacs function number. The way the #virtual site is defined will depend on the function #number, and the number of atoms. #This section HAS to go #after the BEADS section VSITES 7 1,2,3 1   #The next sections specify the bonded terms you #want parametrized, in terms of the corresponding beads. BONDS 1,2 1,3 1,4 4,5 4,6 ANGLES 1,4,5 1,4,6 1,2,4 2,4,5 5,4,2 4,2,1 DIHEDRALS 1,2,4,5 5,4,2,1 IMPROPERS   3,2,1,4 ``` -------------------------------- ### Run Bartender: Replica-Exchange MD Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Perform replica-exchange MD for flexible molecules, specifying the number of replicas and maximum temperature. ```bash # Replica-exchange MD for flexible molecules bartender -re -replicas 8 -maxtemp 450 ligand.xyz bartender.inp ``` -------------------------------- ### Plot XVG Data with Matplotlib Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt This Python script uses matplotlib to plot data from XVG files, skipping lines starting with '@'. It visualizes MD energies and fitted functions, saving the plot as a PNG file. ```python # Plot XVG with matplotlib (skip lines starting with "@") import matplotlib.pyplot as plt import numpy as np data = np.loadtxt("xvg/Angle_Hooke_6-7-8.xvg", comments="@", usecols=(0, 1, 2)) plt.plot(data[:, 0], data[:, 1], "r^", label="MD energies") plt.plot(data[:, 0], data[:, 2], "b-", label="Fitted function") plt.xlabel("Angle (degrees)") plt.ylabel("Energy (kJ/mol)") plt.legend() plt.savefig("angle_6-7-8.png") ``` -------------------------------- ### Run Replica-Exchange MD with Automatic Replica Count Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Launches a temperature replica-exchange simulation using the `ree` utility. This command automatically determines the number of replicas based on available CPUs. ```bash # Automatic replica count (cpus / 3, minimum 5) bartender -re -time 5000 -temperature 310 -maxtemp 450 ligand.xyz bartender.inp ``` -------------------------------- ### Produce Bartender SM3 Topologies Source: https://github.com/martini-force-field-initiative/bartender/blob/master/utils/README.md Merges bonded parameters from Bartender output with bead definitions from reference topologies to create complete Bartender topologies for simulations. Specify the list file, reference folder, and Bartender output folder. ```bash LIST="list_small_mol" REF_FOLDER="reference-COG-itp-2022ATS" BAR_FOLDER="output-Bartender-2022ATS" python produce_bartender_sm3_itps.py -l ${LIST} -r ${REF_FOLDER} -b ${BAR_FOLDER} ``` -------------------------------- ### Compile Bartender from Source (With XTC Support) Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Compile Bartender from source with XTC trajectory support. Requires xdrfile library headers and libraries to be discoverable via C_INCLUDE_PATH and LD_LIBRARY_PATH. ```bash # Requires the xdrfile library headers and libaries to be discoverable # via C_INCLUDE_PATH and LD_LIBRARY_PATH git clone https://github.com/Martini-Force-Field-Initiative/Bartender cd Bartender go build -tags "xtc" ``` -------------------------------- ### Prepare Bartender Input for Toluene Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Generates an input file for Bartender using specified index and itp files. This is the first step before running Bartender for parameterization. ```bash python utils/write_bartender_inp.py \ --ndx utils/inputs/TOLU_oplsaaTOcg_cgbuilder_refined.ndx \ --itp utils/inputs/TOLU.itp \ --out TOLU_bartender.inp ``` -------------------------------- ### Run Bartender: Minimal Invocation Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Generate Martini 3 bonded parameters by running a default 10 ns GFN2-xTB MD simulation and fitting all bonded terms. ```bash # Syntax bartender [FLAGS] geometry_file bartender_input.inp # Minimal invocation — runs a 10 ns GFN2-xTB MD (default) and fits all bonded terms bartender ligand.xyz bartender.inp ``` -------------------------------- ### Run Bartender: Charged Molecule with Solvent Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Run Bartender for a charged molecule, specifying the charge and solvent dielectric. Adjust simulation time as needed. ```bash # Charged molecule, explicit solvent dielectric bartender -charge -1 -solvent h2o -time 5000 ligand.pdb bartender.inp ``` -------------------------------- ### Run Bartender: Re-fit Parameters from Existing Trajectory Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Re-fit bonded parameters from an existing xtb trajectory file without rerunning the MD simulation. ```bash # Re-fit bonded parameters from an existing xtb.trj without rerunning the MD bartender -refit ligand.xyz bartender.inp ``` -------------------------------- ### Run Bartender: Short Test Run Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Perform a short test run of 100 ps, useful for quick checks or on systems with limited resources. ```bash # Short test run (100 ps, useful for laptops / quick checks) bartender -time 100 ligand.xyz bartender.inp ``` -------------------------------- ### Run Bartender for Toluene Parameterization Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Executes Bartender with a generated input file to perform the parameterization. This command assumes the input file has already been created. ```bash bartender -time 10000 toluene.xyz TOLU_bartender.inp ``` -------------------------------- ### Basic Bartender Usage Source: https://github.com/martini-force-field-initiative/bartender/wiki/Home The fundamental command to run Bartender. Provide the geometry file and the input file. Flags should precede other arguments. ```bash bartender [FLAGS] geometry.xyz bartender.inp ``` -------------------------------- ### Merge Bartender Output with Reference Topologies Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Combines Bartender-fitted bonded parameters with bead and virtual-site definitions from a reference CG topology set. This script produces complete `.itp` files ready for simulation. ```bash # Set variables pointing to your molecule list and itp folders LIST="utils/list_small_mol" REF_FOLDER="utils/reference-COG-itp-2022ATS" BAR_FOLDER="utils/output-Bartender-2022ATS" python utils/produce_bartender_sm3_itps.py \ -l ${LIST} \ -r ${REF_FOLDER} \ -b ${BAR_FOLDER} ``` -------------------------------- ### Convert to Bartender Input File Source: https://github.com/martini-force-field-initiative/bartender/wiki/utility-scripts Use this script to convert AA-to-CG mappings and CG topologies into a Bartender input file. Ensure you have the correct .ndx and .itp files. ```bash python write_bartender_inp.py --ndx inputs/BENZ_oplsaaTOcg_cgbuilder.ndx --itp inputs/BENZ_cog.itp --out BENZ_bartender.inp python write_bartender_inp.py --ndx inputs/NDMBI_oplsaaTOcg_cgbuilder.ndx --itp inputs/NDMBI.itp --out NDMBI_bartender.inp python write_bartender_inp.py --ndx inputs/TOLU_oplsaaTOcg_cgbuilder_refined.ndx --itp inputs/TOLU.itp --out TOLU_bartender.inp python write_bartender_inp.py --ndx inputs/PCRE_oplsaaTOcg_cgbuilder.ndx --itp inputs/PCRE.itp --out PCRE_bartender.inp ``` -------------------------------- ### Gromacs Bonded-Parameter Topology (`gmx_out.itp`) Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt This file contains fitted parameters for bonded terms, with only the recommended potential function active and others commented out. Each parameter line includes the fit RMSD. ```text [bonds] ; i j funct length force.c. 3 5 1 0.383 18868.97 ; rmsd: 2.57 5 6 1 0.300 5000.00 ; rmsd: 1.96 10 11 1 0.247 5000.00 ; rmsd: 1.90 [constraints] ; i j funct length 1 2 1 0.205 ; rmsd: 1.41 2 3 1 0.233 ; rmsd: 0.98 6 7 1 0.389 ; rmsd: 1.65 [angles] ; i j k funct angle force_constant 1 2 3 1 145.20 628.64 ; rmsd: 1.28 4 3 5 1 59.75 643.03 ; rmsd: 1.62 ;; 1 2 3 2 144.23 2005.70 ;; Harmonic-Cos (Gromos96) rmsd: 1.07 ; ReB 7 9 10 10 134.77 513.26 ; rmsd: 1.28 5 6 11 10 213.76 54.30 ; rmsd: 2.58 [dihedrals] ; i j k l funct phase kd pn 7 9 10 11 1 188.96 2.32 3 ; rmsd: 0.91 1 5 6 11 1 176.42 5.58 1 ; rmsd: 1.40 ;; 7 9 10 11 3 4.30 1.88 -8.50 -14.83 6.56 13.16 ;; Ryckaert-Belleman's rmsd: 0.54 ;Improper 3 5 6 7 2 133.56 16.37 ; rmsd: 1.69 2 3 4 1 2 0.00 616.64 ; rmsd: 0.96 ``` -------------------------------- ### Plot XVG Data with xmgrace Source: https://github.com/martini-force-field-initiative/bartender/wiki/example Use the xmgrace command-line tool to quickly plot data from XVG files. XVG files contain energy data from MD trajectories in a plain text format. ```bash xmgrace file.xvg ``` -------------------------------- ### Bartender -restart Flag Source: https://github.com/martini-force-field-initiative/bartender/blob/master/README.md Restart an xtb simulation from a previous run. The xtb.trj file must be present. Note that only coordinates are used, not velocities, and the previously run time is discounted. ```bash bartender -restart ``` -------------------------------- ### Bartender -method Flag Source: https://github.com/martini-force-field-initiative/bartender/blob/master/README.md Select the semiempirical method for the simulation. Valid options include gfn0, gfn1, gfn2, and gfnff. Defaults to 'gfn2'. ```bash bartender -method _string_ ``` -------------------------------- ### Running Bartender Command Source: https://github.com/martini-force-field-initiative/bartender/wiki/example This command executes Bartender with a specified simulation time and input files. The '-time' flag sets a short simulation duration for quick testing. Ensure the flag precedes the geometry and input file arguments. ```bash bartender -time 100 ligand.xyz bartender.inp ``` -------------------------------- ### Bartender -time Flag Source: https://github.com/martini-force-field-initiative/bartender/blob/master/README.md Set the total simulation time for QM MD in picoseconds (ps). A negative value will skip MD and use a previous trajectory. ```bash bartender -time _int_ ``` -------------------------------- ### Run Bartender Command Source: https://github.com/martini-force-field-initiative/bartender/blob/master/README.md Basic command to run Bartender. Ensure Bartender and xtb executables are in your PATH. The geometry file can be in XYZ, PDB, or GRO format. ```bash bartender [flags] Geometry.xyz BartenderInput.inp ``` -------------------------------- ### Run Bartender with Verbosity and Custom Plot Directory Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Execute Bartender with increased verbosity and specify a custom directory for output plots. This command initiates a simulation using a ligand structure and a Bartender input file. ```bash bartender -v 3 -plotdir ./plots ligand.xyz bartender.inp ``` -------------------------------- ### Run Bartender: Use Pre-existing Trajectory Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Utilize a pre-existing trajectory file (e.g., DCD) instead of running a new MD simulation. ```bash # Use a pre-existing trajectory instead of running a new MD bartender -owntraj my_trajectory.dcd ligand.xyz bartender.inp ``` -------------------------------- ### Run Bartender: Save DCD Trajectory Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Run Bartender and save the generated xtb trajectory in DCD format for later reuse. ```bash # Save xtb trajectory as DCD for later reuse bartender -dcdSave traj.dcd -time 10000 ligand.xyz bartender.inp ``` -------------------------------- ### Run Bartender with Custom Fitting Thresholds Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt This bash command demonstrates how to run Bartender using a custom 'goodenough' file to override default acceptance criteria for RMSD and force-constant ranges per bonded term type. ```bash # Run with a custom goodenough file bartender -goodenoughfile my_thresholds.ge ligand.xyz bartender.inp ``` -------------------------------- ### Grace XVG Data Format Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt Plain-text files in Grace format containing energy and fitted-function data. Units are kJ/mol versus Ångströms for bonds, or degrees for other terms. These files complement the PNG fit plots. ```text @ xaxis label "Length or angle (A or deg)" @ yaxis label "Energy (kJ/mol)" @TYPE xy 52.825210 8.851045 10.143528 53.825210 8.851045 7.680327 54.825210 6.019390 5.559174 60.825210 -0.00000 0.015255 ... ``` -------------------------------- ### Custom Fitting Thresholds File Format (`goodenough.ge`) Source: https://context7.com/martini-force-field-initiative/bartender/llms.txt The 'goodenough' file allows customization of fitting thresholds. Each line specifies the term type (dihe, angles, impropers, bonds) followed by min/max force constants and max RMSD values for different potential functions. ```text # Format: # dihe k_min k_max rmsd_max_SimplePeriodic rmsd_max_RyckaertBellemans # angles k_min k_max rmsd_max # impropers k_min k_max rmsd_max # bonds k_min k_max rmsd_max dihe 0.5 200 5.0 3.0 angles 10 5000 4.0 impropers 5 2000 5.0 bonds 100 500000 3.0 ``` -------------------------------- ### Configure Goodenough File Parameters Source: https://github.com/martini-force-field-initiative/bartender/blob/master/README.md Format for the 'Goodenough' file, used to specify maximum acceptable RMSD values and ranges for force constants for different bond term types. ```plaintext dihe k v1 v2 rmsd v3 v4 angles k v1 v2 rmsd v3 impropers k v1 v2 rmsd v3 bonds k v1 v2 rmsd v3 ``` -------------------------------- ### Dihedral Parameters in Bartender Source: https://github.com/martini-force-field-initiative/bartender/wiki/example Shows dihedral angle parameters, including periodic, Ryckaert-Bellemans, and combined bending-torsion potentials. Note that angles approaching 180 degrees can cause simulation instability. ```text [dihedrals] ; i j k l funct phase kd pn 7 9 10 11 1 188.96 2.32 3 ; rmsd: 0.91 1 5 6 11 1 176.42 5.58 1 ; rmsd: 1.40 ;; 7 9 10 11 3 4.30 1.88 -8.50 -14.83 6.56 13.16 ;; Ryckaert-Belleman's potential. rmsd: 0.54 ;; 1 5 6 11 3 10.04 0.53 -7.43 18.73 1.79 -16.04 ;; Ryckaert-Belleman's potential. rmsd: 1.13 ;; 7 9 10 11 11 22053.80 4534.87 4460.29 4525.27 4444.57 4300.94 ;; Combined bending-torsion potential. rmsd: 0.76 ``` -------------------------------- ### Bartender -owntraj Flag Source: https://github.com/martini-force-field-initiative/bartender/blob/master/README.md Read a trajectory file (DCD, XTC, multiPDB, or multiXYZ) instead of performing an xtb simulation. The file type is identified by its extension. ```bash bartender -owntraj _filename_ ```