### Compile and Install PLUMED Source: https://www.plumed.org/doc-v2.10/user-doc/html/_installation.html Standard commands to configure, compile, and install PLUMED. `make install` is optional but recommended for a full setup. `make doc` is optional and requires doxygen. ```bash > ./configure --prefix=/usr/local > make -j 4 > make doc # this is optional and requires proper doxygen version installed > make install ``` -------------------------------- ### Multi-replica INCLUDE Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_i_n_c_l_u_d_e.html This example illustrates how the INCLUDE action is used in a multi-replica simulation setup, where different replicas include different files. ```plumed #SETTINGS NREPLICAS=2 **t: **TORSION ATOMS=1,2,3,4 INCLUDE FILE=other.inc ``` -------------------------------- ### Generate Example for Manual Source: https://www.plumed.org/doc-v2.10/user-doc/html/tools.html Use the 'gen_example' tool to create interactive examples for the PLUMED manual. ```bash plumed gen_example ``` -------------------------------- ### Bias Exchange Metadynamics Setup with @replicas: Source: https://www.plumed.org/doc-v2.10/user-doc/html/special-replica-syntax.html This example illustrates setting up a bias exchange metadynamics simulation using the `@replicas:` syntax for replica-dependent parameters. It shows how to compute a distance and apply a restraint with different centers for each replica. ```plumed #SETTINGS NREPLICAS=2 # Compute distance between atoms 1 and 2 **d: **DISTANCE ATOMSthe pair of atom that we are calculating the distance between. __=1,2 The DISTANCE action with label **d** calculates a single scalar value ``` -------------------------------- ### WHAM Histogram Analysis Setup Source: https://www.plumed.org/doc-v2.10/user-doc/html/_w_h_a_m__h_i_s_t_o_g_r_a_m.html This example demonstrates the setup for analyzing umbrella sampling data using WHAM. It defines torsion angles, applies restraints, and prepares for histogram calculation. Ensure PLUMED is configured with --enable-modules=wham. ```text #SETTINGS NREPLICAS=4 **phi: **TORSION ATOMSthe four atoms involved in the torsional angle __=5,7,9,15 The TORSION action with label **phi** calculates a single scalar value **psi: **TORSION ATOMSthe four atoms involved in the torsional angle __=7,9,15,17 The TORSION action with label **psi** calculates a single scalar value **rp: **RESTRAINT ARGthe arguments on which the bias is acting. __=**phi** KAPPA**compulsory keyword ( default=0.0 )** specifies that the restraint is harmonic and what the values of the force constants on each of the variables are __=50.0 AT**compulsory keyword ** the position of the restraint __=@replicas:{ -3.00000000000000000000 -1.45161290322580645168 .09677419354838709664 1.64516129032258064496 } ...The RESTRAINT action with label **rp** calculates the following quantities: ** Quantity ** | ** Description ** ---|--- rp.bias| the instantaneous value of the bias potential rp.force2| the instantaneous value of the squared force due to this bias potential ``` -------------------------------- ### Configure and install PLUMED Source: https://www.plumed.org/doc-v2.10/user-doc/html/_installation.html This sequence of commands configures PLUMED with a specified installation prefix, compiles it, and then installs it. Ensure you have the necessary permissions if installing to a system directory. ```bash > ./configure --prefix=$HOME/opt > make > make install ``` -------------------------------- ### ECV_MULTITHERMAL with TEMP_MAX Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_e_c_v__m_u_l_t_i_t_h_e_r_m_a_l.html Example of ECV_MULTITHERMAL action specifying the maximum temperature. ```text **ecv: **ECV_MULTITHERMAL ARG**compulsory keyword ** the label of the internal energy of the system. __=intEne TEMP_MAXthe maximum of the temperature range __=800 The ECV_MULTITHERMAL action with label **ecv** ``` -------------------------------- ### TD_CHISQUARED Action Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_t_d__c_h_i_s_q_u_a_r_e_d.html This example demonstrates the basic usage of the TD_CHISQUARED action with specified minimum, sigma, and kappa values. Ensure the vesmodule is configured. ```text **td: **TD_CHISQUARED MINIMUM**compulsory keyword ** The minimum of the chi-squared distribution. __=-10.0 SIGMA**compulsory keyword ** The sigma parameter of the chi-squared distribution given as a positive number. __=2.0 KAPPA**compulsory keyword ** The k parameter of the chi-squared distribution given as positive integer larger than 2. __=2 The TD_CHISQUARED action with label **td** ``` -------------------------------- ### CS2BACKBONE: CAshifts.dat Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_c_s2_b_a_c_k_b_o_n_e.html Example format for the CAshifts.dat file used by CS2BACKBONE. It specifies chemical shifts for backbone carbons, with '#' indicating the start/end of chains. ```text #1 0.0 2 55.5 3 58.4 . . #last 0.0 #first of second chain . #last of second chain ``` -------------------------------- ### Get PLUMED Root Directory Source: https://www.plumed.org/doc-v2.10/user-doc/html/info.html Use this command to find the installation path of your PLUMED distribution. No additional setup is required. ```bash plumed info --root ``` -------------------------------- ### ADAPTIVE_PATH Configuration Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_a_d_a_p_t_i_v_e__p_a_t_h.html This example shows a typical configuration for the ADAPTIVE_PATH action, specifying the type of path calculation, fixed nodes, update frequency, and output file. ```text pp: ADAPTIVE_PATH TYPE=EUCLIDEAN FIXED=2,5 UPDATE=50 WFILE=out-path.pdb WSTRIDE=50 REFERENCE=mypath.pdb ``` -------------------------------- ### KDE and Histogram Calculation with Dump Source: https://www.plumed.org/doc-v2.10/user-doc/html/_d_u_m_p_g_r_i_d.html This example sets up a workflow to calculate kernel density estimation (KDE) for two torsional angles, combine it with a weight, and then dump the resulting grid. It involves defining torsions, calculating KDE, custom function evaluation, accumulation, and finally dumping the grid. ```text **r1: **TORSION ATOMSthe four atoms involved in the torsional angle __=1,2,3,4 The TORSION action with label **r1** calculates a single scalar value **r2: **TORSION ATOMSthe four atoms involved in the torsional angle __=2,3,4,5 The TORSION action with label **r2** calculates a single scalar value **hh_weight: **ONES SIZE**compulsory keyword ** the number of ones that you would like to create __=1 The ONES action with label **hh_weight** calculates a single scalar value **hh_kde: **KDE ARGthe input for this action is the scalar output from one or more other actions. __=**r1**,**r2** GRID_MIN**compulsory keyword ( default=auto )** the lower bounds for the grid __=-3.14,-3.14 GRID_MAX**compulsory keyword ( default=auto )** the upper bounds for the grid __=3.14,3.14 GRID_BINthe number of bins for the grid __=200,200 BANDWIDTHthe bandwidths for kernel density esimtation __=0.05,0.05 The KDE action with label **hh_kde** calculates a single scalar value **hh_kdep: **CUSTOM ARGthe input to this function. __=**hh_kde**,**hh_weight** FUNC**compulsory keyword ** the function you wish to evaluate __=x*y PERIODIC**compulsory keyword ** if the output of your function is periodic then you should specify the periodicity of the function. __=NO The CUSTOM action with label **hh_kdep** calculates a single scalar value **hh_u: **ACCUMULATE ARGthe input for this action is the scalar output from one or more other actions. __=**hh_kdep** STRIDE**compulsory keyword ( default=1 )** the frequency with which the data should be collected and added to the quantity being averaged __=1 CLEAR**compulsory keyword ( default=0 )** the frequency with which to clear all the accumulated data. __=0 The ACCUMULATE action with label **hh_u** calculates a single scalar value **hh_nsum: **ACCUMULATE ARGthe input for this action is the scalar output from one or more other actions. __=**hh_weight** STRIDE**compulsory keyword ( default=1 )** the frequency with which the data should be collected and added to the quantity being averaged __=1 CLEAR**compulsory keyword ( default=0 )** the frequency with which to clear all the accumulated data. __=0 The ACCUMULATE action with label **hh_nsum** calculates a single scalar value **hh: **CUSTOM ARGthe input to this function. __=**hh_u**,**hh_nsum** FUNC**compulsory keyword ** the function you wish to evaluate __=x/y PERIODIC**compulsory keyword ** if the output of your function is periodic then you should specify the periodicity of the function. __=NO The CUSTOM action with label **hh** calculates a single scalar value DUMPGRID GRIDthe grid you would like to print (can also use ARG for specifying what is being printed) __=**hh** FILE**compulsory keyword ( default=density )** the file on which to write the grid. __=histo The DUMPGRID action with label **** ``` -------------------------------- ### Get PLUMED Root Directory Source: https://www.plumed.org/doc-v2.10/user-doc/html/_installation.html Displays the hard-coded root directory of the PLUMED installation. This is useful for understanding dependencies. ```bash > plumed info --root ``` -------------------------------- ### Create a Sample plumed.dat File Source: https://www.plumed.org/doc-v2.10/user-doc/html/benchmark.html This example shows how to create a basic plumed.dat file for testing. It includes WHOLEMOLECULES, POSITION, and RESTRAINT actions. ```bash WHOLEMOLECULES ENTITY0the atoms that make up a molecule that you wish to align. __=1-10000 The WHOLEMOLECULES action with label **** **p: **POSITION ATOMthe atom number. __=1 The POSITION action with label **p** calculates the following quantities: ** Quantity ** | ** Description ** ---|--- p.x| the x-component of the atom position p.y| the y-component of the atom position p.z| the z-component of the atom position RESTRAINT ARGthe arguments on which the bias is acting. __=**p.x** KAPPA**compulsory keyword ( default=0.0 )** specifies that the restraint is harmonic and what the values of the force constants on each of the variables are __=1 AT**compulsory keyword ** the position of the restraint __=0 The RESTRAINT action with label **** ``` -------------------------------- ### TD_PRODUCT_COMBINATION Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_t_d__p_r_o_d_u_c_t__c_o_m_b_i_n_a_t_i_o_n.html This example demonstrates how to use TD_PRODUCT_COMBINATION to create a target distribution by combining a well-tempered distribution with a uniform distribution that decays to zero. This effectively cuts off the tail of the well-tempered distribution. ```text **td_welltemp: **TD_WELLTEMPERED BIASFACTOR**compulsory keyword ** The bias factor used for the well-tempered distribution. __=5 The TD_WELLTEMPERED action with label **td_welltemp** **td_uniform: **TD_UNIFORM MINIMAThe minimum of the intervals where the target distribution is taken as uniform. __=0.23 MAXIMAThe maximum of the intervals where the target distribution is taken as uniform. __=0.6 SIGMA_MAXIMAThe standard deviation parameters of the Gaussian switching functions for the maximum of the intervals. __=0.05 The TD_UNIFORM action with label **td_uniform** **td_combination: **TD_PRODUCT_COMBINATION DISTRIBUTIONS**compulsory keyword ** The labels of the target distribution actions to be used in the product combination. __=**td_uniform**,**td_welltemp** The TD_PRODUCT_COMBINATION action with label **td_combination** ``` -------------------------------- ### Enable Bash Autocompletion for PLUMED with MPI Source: https://www.plumed.org/doc-v2.10/user-doc/html/_bash_autocompletion.html Source this function in your bash profile to enable autocompletion for the `plumed_mpi` command. This setup is for MPI-enabled PLUMED installations. ```bash _plumed_mpi() { eval "$(plumed_mpi --no-mpi completion 2>/dev/null)";} complete -F _plumed_mpi -o default plumed_mpi ``` -------------------------------- ### Generate Example from PLUMED File Source: https://www.plumed.org/doc-v2.10/user-doc/html/gen_example.html Use this command to generate an HTML example based on the contents of a PLUMED input file. The `--status working` flag indicates that the input file is functional. ```bash plumed gen_example --plumed plumed.dat --status working ``` -------------------------------- ### Funnel Potential Calculation Source: https://www.plumed.org/doc-v2.10/user-doc/html/_f_u_n_n_e_l.html Example PLUMED input for calculating a funnel-shaped restraint potential. This setup uses FUNNEL_PS to define the collective variables and specifies parameters for the funnel's shape and resolution. ```text **lig: **COM ATOMSthe list of atoms which are involved the virtual atom's definition. __=3221,3224,3225,3228,3229,3231,3233,3235,3237 You cannot view the components that are calculated by each action for this input file. Sorry **fps: **FUNNEL_PS LIGANDThis MUST be a single atom, normally the COM of the ligand. __=**lig** REFERENCE**compulsory keyword ** a file in pdb format containing the structure you would like to align. __=start.pdb ANCHORClosest protein atom to the ligand, picked to avoid pbc problems during the simulation. __=2472 POINTS**compulsory keyword ** 6 values defining x, y, and z of the 2 points used to construct the line. __=4.724,5.369,4.069,4.597,5.721,4.343 You cannot view the components that are calculated by each action for this input file. Sorry **funnel: **FUNNEL ARGthe input for this action is the scalar output from one or more other actions. __=**fps.lp**,**fps.ld** ZCC**compulsory keyword ( default=ZCC )** switching point between cylinder and cone __=1.8 ALPHAangle to change the width of the cone section __=0.55 RCYLradius of the cylindrical section __=0.1 MINSminimum value assumed by fps.lp, __=-0.5 MAXS**compulsory keyword ( default=MAXS )** maximum value assumed by fps.lp __=3.7 KAPPAconstant to be used for the funnel-shape restraint potential __=35100 NBINSnumber of bins along fps.lp __=500 NBINZnumber of bins along fps.ld __=500 FILE**compulsory keyword ** name of the Funnel potential file __=BIAS You cannot view the components that are calculated by each action for this input file. Sorry ``` -------------------------------- ### Example: Splitting Input into Two Files Source: https://www.plumed.org/doc-v2.10/user-doc/html/includes.html Demonstrates how to split a PLUMED input file into a main file and an included file using the INCLUDE directive. ```plumed **dist: **DISTANCE ATOMSthe pair of atom that we are calculating the distance between. __=1,2 The DISTANCE action with label **dist** calculates a single scalar value INCLUDE FILE**compulsory keyword ** file to be included __=toBeIncluded.inc The INCLUDE action with label **** ``` ```plumed #SETTINGS FILENAME=toBeIncluded.inc # this is toBeIncluded.inc RESTRAINT ARGthe arguments on which the bias is acting. __=dist AT**compulsory keyword ** the position of the restraint __=2.0 KAPPA**compulsory keyword ( default=0.0 )** specifies that the restraint is harmonic and what the values of the force constants on each of the variables are __=1.0 You cannot view the components that are calculated by each action for this input file. Sorry ``` -------------------------------- ### Configure Bash Autocompletion for PLUMED Source: https://www.plumed.org/doc-v2.10/user-doc/html/_bash_autocompletion.html Add these lines to your `.bashrc` file to enable PLUMED command and option autocompletion using the TAB key. This setup allows for dynamic completion based on the installed PLUMED version. ```bash _plumed() { eval "$(plumed --no-mpi completion 2>/dev/null)";} complete -F _plumed -o default plumed ``` -------------------------------- ### ECV_LINEAR and OPES_EXPANDED Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_e_c_v__l_i_n_e_a_r.html Example configuration for ECV_LINEAR and OPES_EXPANDED actions. ECV_LINEAR calculates a Hamiltonian difference, and OPES_EXPANDED uses this to perform expanded sampling. ```text **ecv: **ECV_LINEAR ARG**compulsory keyword ** the label of the Hamiltonian difference. __=**DeltaU** TEMP**compulsory keyword ( default=-1 )** temperature. __=300 The ECV_LINEAR action with label **ecv** calculates a single scalar value **opes: **OPES_EXPANDED ARG**compulsory keyword ** the label of the ECVs that define the expansion. __=**ecv.*** PACE**compulsory keyword ** how often the bias is updated __=100 The OPES_EXPANDED action with label **opes** calculates a single scalar value ``` -------------------------------- ### Minimal Working Example of OPES_METAD_EXPLORE Source: https://www.plumed.org/doc-v2.10/user-doc/html/_o_p_e_s__m_e_t_a_d__e_x_p_l_o_r_e.html This is a minimal example demonstrating the usage of the OPES_METAD_EXPLORE action. It requires a collective variable (cv) and defines the frequency of kernel deposition and the free energy barrier. ```text **cv: **DISTANCE ATOMSthe pair of atom that we are calculating the distance between. __=1,2 The DISTANCE action with label **cv** calculates a single scalar value **opes: **OPES_METAD_EXPLORE ARGthe input for this action is the scalar output from one or more other actions. __=**cv** PACE**compulsory keyword ** the frequency for kernel deposition __=500 BARRIER**compulsory keyword ** the free energy barrier to be overcome. __=40 The OPES_METAD_EXPLORE action with label **opes** calculates the following quantities: ** Quantity ** | ** Description ** ---|--- opes.bias| the instantaneous value of the bias potential opes.rct| estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting opes.zed| estimate of Z_n. should become flat once no new CV-space region is explored opes.neff| effective sample size opes.nker| total number of compressed kernels used to represent the bias PRINT STRIDE**compulsory keyword ( default=1 )** ``` -------------------------------- ### Steered MD: Restraining Distance Between Atoms Source: https://www.plumed.org/doc-v2.10/user-doc/html/_m_o_v_i_n_g_r_e_s_t_r_a_i_n_t.html This example demonstrates how to use MOVINGRESTRAINT to steer the distance between two atoms. The restraint starts at 1.0, moves to 2.0 over 1000 steps, returns to 1.0 over the next 1000 steps, and is then switched off over 500 steps. ```plumed **d: **DISTANCE ATOMSthe pair of atom that we are calculating the distance between. __=2,4 The DISTANCE action with label **d** calculates a single scalar value MOVINGRESTRAINT ... ARGthe input for this action is the scalar output from one or more other actions. __=**d** STEP0**compulsory keyword ** This keyword appears multiple times as STEPx with x=0,1,2,...,n. __=0 AT0**compulsory keyword ** ATx is equal to the position of the restraint at time STEPx. __=1.0 KAPPA0**compulsory keyword ** KAPPAx is equal to the value of the force constants at time STEPx. __=100.0 STEP1**compulsory keyword ** This keyword appears multiple times as STEPx with x=0,1,2,...,n. __=1000 AT1**compulsory keyword ** ATx is equal to the position of the restraint at time STEPx. __=2.0 STEP2**compulsory keyword ** This keyword appears multiple times as STEPx with x=0,1,2,...,n. __=2000 AT2**compulsory keyword ** ATx is equal to the position of the restraint at time STEPx. __=1.0 STEP3**compulsory keyword ** This keyword appears multiple times as STEPx with x=0,1,2,...,n. __=2500 KAPPA3**compulsory keyword ** KAPPAx is equal to the value of the force constants at time STEPx. __=0.0 ...The MOVINGRESTRAINT action with label **** ``` -------------------------------- ### Enable Restart with Default File Handling Source: https://www.plumed.org/doc-v2.10/user-doc/html/_r_e_s_t_a_r_t.html This example shows the basic usage of the RESTART directive. When a simulation restarts, existing output files will be automatically backed up. ```plumed **d: **DISTANCE ATOMSthe pair of atom that we are calculating the distance between. __=1,2 The DISTANCE action with label **d** calculates a single scalar value PRINT ARGthe input for this action is the scalar output from one or more other actions. __=**d** FILEthe name of the file on which to output these quantities __=out The PRINT action with label **** ``` -------------------------------- ### Install PLUMED with MacPorts Source: https://www.plumed.org/doc-v2.10/user-doc/html/_installation.html Basic installation of PLUMED using MacPorts on macOS. Ensure MacPorts is installed first. ```bash sudo port install plumed ``` -------------------------------- ### Simulated Tempering with SELECT and PBMETAD Source: https://www.plumed.org/doc-v2.10/user-doc/html/_s_e_l_e_c_t.html This example demonstrates a simulated-tempering approach using RESCALE, PBMETAD, and SELECT. It shows how to activate independent PBMETAD simulations based on a SELECTOR's value and use SELECT to output the active bias potential. Ensure SELECTOR and PBMETAD actions are correctly configured. ```plumed ene: ENERGY d: DISTANCE ATOMS=1,2 GAMMA: SELECTOR pbmetad0: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=0 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.0 pbmetad1: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=1 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.1 res: RESCALE ARG=ene,pbmetad0.bias,pbmetad1.bias TEMP=300 SELECTOR=GAMMA MAX_RESCALE=1.2 NOT_RESCALED=2 NBIN=2 W0=1000 BIASFACTOR=100.0 BSTRIDE=2000 BFILE=bias.dat ``` -------------------------------- ### Install metatomic-torch with pip Source: https://www.plumed.org/doc-v2.10/user-doc/html/_m_e_t_a_t_o_m_i_c_m_o_d.html Installs the metatomic-torch Python wheel. Adjust the version number as needed. After installation, use the provided script to obtain C++ compiler and linker flags. ```bash pip install "metatomic-torch ==0.1.0" # change this version to get newer releases # you can then get the compiler and linker flags using the script at # src/metatomic/flags-from-python.py CPPFLAGS=$(python src/metatomic/flags-from-python.py --cppflags) LDFLAGS=$(python src/metatomic/flags-from-python.py --ldflags) ``` -------------------------------- ### Install PLUMED Python Wrappers using pip Source: https://www.plumed.org/doc-v2.10/user-doc/html/_installation.html This is the simplest method for installing Python wrappers separately from PLUMED, especially if you use multiple Python versions. The `--user` flag installs packages in your home directory. You may need to set the PLUMED_KERNEL environment variable to point to the PLUMED installation. ```bash pip3.6 install --user plumed export PLUMED_KERNEL=$HOME/opt/lib/libplumedKernel.so python3.6 >>> import plumed ``` -------------------------------- ### PRINT Action Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_f_i_s_s_t.html This example demonstrates the usage of the PRINT action to output scalar quantities from other actions. It specifies the input arguments, output file, and stride for data collection. ```text PRINT ARGthe input for this action is the scalar output from one or more other actions. __=**dend**,**f.dend_fbar**,**f.bias**,**f.force2** FILEthe name of the file on which to output these quantities __=pull.colvar.txt STRIDE**compulsory keyword ( default=1 )** the frequency with which the quantities of interest should be output __=1000 The PRINT action with label **** ``` -------------------------------- ### GPROPERTYMAP Action Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_g_p_r_o_p_e_r_t_y_m_a_p.html This example demonstrates how to use the GPROPERTYMAP action to calculate interpolated property values (X and Y) based on reference configurations. It specifies the reference PDB file, the properties to interpolate, and the LAMBDA parameter. The distance metric used is the OPTIMAL metric. ```text **p2: **GPROPERTYMAP REFERENCE**compulsory keyword ** a pdb file containing the set of reference configurations __=allv.pdb PROPERTYthe property to be used in the index. __=X,Y LAMBDA**compulsory keyword ** ``` -------------------------------- ### Configure and Install PLUMED with Python Wrappers Source: https://www.plumed.org/doc-v2.10/user-doc/html/_installation.html Use this method when you want to install Python wrappers as part of your PLUMED installation. Ensure the Python interpreter has the 'cython' module available. The directory containing the wrappers will be added to PYTHONPATH. ```bash ./configure PYTHON_BIN=python3.6 --prefix=$HOME/opt make && make install export PYTHONPATH="$HOME/opt/lib/plumed/python:$PYTHONPATH" python3.6 >>> import plumed ``` -------------------------------- ### TD_CHISQUARED with TD_PRODUCT_DISTRIBUTION Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_t_d__c_h_i_s_q_u_a_r_e_d.html This example shows how to use TD_CHISQUARED for one dimension in conjunction with TD_UNIFORM and TD_PRODUCT_DISTRIBUTION to create a multi-dimensional target distribution. Ensure the vesmodule is configured. ```text **td_chisq: **TD_CHISQUARED MINIMUM**compulsory keyword ** The minimum of the chi-squared distribution. __=10.0 SIGMA**compulsory keyword ** The sigma parameter of the chi-squared distribution given as a positive number. __=2.0 KAPPA**compulsory keyword ** The k parameter of the chi-squared distribution given as positive integer larger than 2. __=2 The TD_CHISQUARED action with label **td_chisq** **td_uni: **TD_UNIFORM The TD_UNIFORM action with label **td_uni** **td_pd: **TD_PRODUCT_DISTRIBUTION DISTRIBUTIONS**compulsory keyword ** Labels of the one-dimensional target distribution actions for each argument to be used in the product distribution. __=**td_chisq**,**td_uni** The TD_PRODUCT_DISTRIBUTION action with label **td_pd** ``` -------------------------------- ### PDB File Content Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_f_u_n_c_p_a_t_h_m_s_d.html Example content of a PDB file used for defining reference coordinates. ```pdb ATOM 1 CL ALA 1 -3.171 0.295 2.045 1.00 1.00 ATOM 5 CLP ALA 1 -1.819 -0.143 1.679 1.00 1.00 ATOM 6 OL ALA 1 -1.177 -0.889 2.401 1.00 1.00 ATOM 7 NL ALA 1 -1.313 0.341 0.529 1.00 1.00 ATOM 8 HL ALA 1 -1.845 0.961 -0.011 1.00 1.00 END ``` ```pdb ATOM 1 CL ALA 1 -3.089 1.850 1.546 1.00 1.00 ATOM 5 CLP ALA 1 -1.667 1.457 1.629 1.00 1.00 ATOM 6 OL ALA 1 -0.974 1.868 2.533 1.00 1.00 ATOM 7 NL ALA 1 -1.204 0.683 0.642 1.00 1.00 ATOM 8 HL ALA 1 -1.844 0.360 -0.021 1.00 1.00 END ``` ```pdb ATOM 1 CL ALA 1 -3.257 1.605 1.105 1.00 1.00 ATOM 5 CLP ALA 1 -1.941 1.459 0.447 1.00 1.00 ATOM 6 OL ALA 1 -1.481 2.369 -0.223 1.00 1.00 ATOM 7 NL ALA 1 -1.303 0.291 0.647 1.00 1.00 ATOM 8 HL ALA 1 -1.743 -0.379 1.229 1.00 1.00 END ``` -------------------------------- ### Install Development Version of PLUMED Python Wrappers with pip Source: https://www.plumed.org/doc-v2.10/user-doc/html/_installation.html To install the development version of the Python wrappers, first clone the PLUMED repository. Ensure 'cython' is installed. This method is recommended within a virtual environment to avoid conflicts with released packages. ```bash pip3.6 install --user cython cd plumed2/python make pip pip3.6 install --user . ``` -------------------------------- ### Target Distribution Grid File Format Source: https://www.plumed.org/doc-v2.10/user-doc/html/_m_e_t_a_d.html Example format for a target distribution grid file. It must include the target free energy and its derivatives, along with metadata like bounds and number of bins. ```text #! FIELDS d1 t1.target der_d1 #! SET min_d1 1.14 #! SET max_d1 1.32 #! SET nbins_d1 6 #! SET periodic_d1 false 1.1400 0.0031 0.1101 1.1700 0.0086 0.2842 1.2000 0.0222 0.6648 1.2300 0.0521 1.4068 1.2600 0.1120 2.6873 1.2900 0.2199 4.6183 1.3200 0.3948 7.1055 ``` -------------------------------- ### ADAPTIVE_PATH Action Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_a_d_a_p_t_i_v_e__p_a_t_h.html Configures the ADAPTIVE_PATH action for calculating distances, specifying update frequency, output file, and reference configurations. ```text **pp: **ADAPTIVE_PATH TYPE**compulsory keyword ( default=OPTIMAL-FAST )** the manner in which distances are calculated. __=EUCLIDEAN FIXED**compulsory keyword ** the positions in the list of input frames of the two path nodes whose positions remain fixed during the path optimization __=2,5 UPDATE**compulsory keyword ** the frequency with which the path should be updated __=50 WFILEfile on which to write out the path __=out-path.pdb WSTRIDE**compulsory keyword ( default=0, )** frequency with which to write out the path __=50 REFERENCE**compulsory keyword ** a pdb file containing the set of reference configurations __=mypath.pdb The ADAPTIVE_PATH action with label **pp** calculates the following quantities: ** Quantity ** | ** Description ** --- pp.s| In the case above the distance between frames is calculated based on the \(x\) and \(y\) components of the vector connecting atoms 1 and 2. As such an extract from the input reference path (mypath.pdb) would look as follows: ``` -------------------------------- ### Install GROMACS patched with PLUMED Source: https://www.plumed.org/doc-v2.10/user-doc/html/_installation.html Install GROMACS patched with PLUMED using MacPorts, ensuring matching compiler variants. ```bash > sudo port install plumed +mpich +clang50 > sudo port install gromacs-plumed +mpich +clang50 ``` -------------------------------- ### Running PLUMED driver-float Source: https://www.plumed.org/doc-v2.10/user-doc/html/driver-float.html This example shows how to run the driver-float command, specifying the PLUMED input file and the trajectory file. ```bash plumed driver-float --plumed plumed.dat --ixyz trajectory.xyz ``` -------------------------------- ### Reference PDB Structure Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_p_o_s_i_t_i_o_n.html An example of a PDB file format used to specify reference structures for the FIT_TO_TEMPLATE action. ```pdb ATOM 3 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O END ``` -------------------------------- ### Load Custom Action and Use Source: https://www.plumed.org/doc-v2.10/user-doc/html/_l_o_a_d.html This example demonstrates how to load a custom DISTANCE action from a file named Distance.so and then use it. The LOAD action affects only subsequent commands. ```text # compute standard distance **d: **DISTANCE ATOMSthe pair of atom that we are calculating the distance between. __=1,10 You cannot view the components that are calculated by each action for this input file. Sorry # load the new definition LOAD FILE**compulsory keyword ** file to be loaded __=Distance.so You cannot view the components that are calculated by each action for this input file. Sorry # compute modified distance **d2: **DISTANCE ATOMSthe pair of atom that we are calculating the distance between. __=1,10 You cannot view the components that are calculated by each action for this input file. Sorry # print them on a file PRINT ARGthe input for this action is the scalar output from one or more other actions. __=**d**,**d2** FILEthe name of the file on which to output these quantities __=compare-them You cannot view the components that are calculated by each action for this input file. Sorry ``` -------------------------------- ### COORDINATIONNUMBER Action Example Source: https://www.plumed.org/doc-v2.10/user-doc/html/_multicolvar.html Example of using the COORDINATIONNUMBER action for calculating coordination numbers with switching functions and a MORE_THAN condition. ```plumed COORDINATIONNUMBER SPECIESthis keyword is used for colvars such as coordination number. __=1-100 SWITCHthe switching function that it used in the construction of the contact matrix __={RATIONAL R_0=1. D_MAX=3.0} MORE_THANcalculate the number of variables that are more than a certain target value. __={RATIONAL R_0=6.0 NN=6 MM=12 D_0=0} The COORDINATIONNUMBER action with label **** ``` -------------------------------- ### Backup and Concatenate Files on Restart Source: https://www.plumed.org/doc-v2.10/user-doc/html/_r_e_s_t_a_r_t.html This example demonstrates backing up 'out1' and concatenating 'out2' when restarting. It uses per-action RESTART=NO for 'out1' and default behavior for 'out2'. ```plumed RESTART The RESTART action with label **** **d1: **DISTANCE ATOMSthe pair of atom that we are calculating the distance between. __=1,2 The DISTANCE action with label **d1** calculates a single scalar value **d2: **DISTANCE ATOMSthe pair of atom that we are calculating the distance between. __=1,2 The DISTANCE action with label **d2** calculates a single scalar value PRINT ARGthe input for this action is the scalar output from one or more other actions. __=**d1** FILEthe name of the file on which to output these quantities __=out1 The PRINT action with label **** PRINT ARGthe input for this action is the scalar output from one or more other actions. __=**d2** FILEthe name of the file on which to output these quantities __=out2 The PRINT action with label **** ```