PLUMED-NEST

Project ID: plumID:26.004
Source: plumed/plumed-funnelmetaD-site2.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

#RESTART

# --- (1) ATOM DEFINITIONS AND ALIGNMENTS ---

# Define groups
prot: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-8297
The GROUP action with label prot calculates somethingligand: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=8298-8329
The GROUP action with label ligand calculates somethinganchor_atom: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1499
The GROUP action with label anchor_atom calculates somethingwater: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=8330-75499:3
The GROUP action with label water calculates somethingene: ENERGYCalculate the total potential energy of the simulation box. More details

# Make protein whole and ensure ligand stays with protein
The ENERGY action with label ene calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=prot
The WHOLEMOLECULES action with label  calculates somethingWRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=ligand AROUNDreference atoms=anchor_atom GROUPBY group atoms so as not to break molecules=32

# --- (2) DESCRIPTORS ---

# All actual descriptors to be used in the DeepTICA training to start with d_
# Definition of ligand heavy atoms COM and 3 potential binding sites CA atoms
COM_L: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=8298-8319
The COM action with label COM_L calculates somethingCOM_B: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=185,243,670,687,709,1350,1370,5246,5257,5276,5282,5308,5314

# Descriptor - distance between COM of QUE and COM of binding sites
The COM action with label COM_B calculates somethingd_L_B: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_L,COM_B

# Water coordination of oxygen atoms on QUE
The DISTANCE action with label d_L_B calculates the following quantities:
 Quantity   
 Description  
d_L_B.value
the DISTANCE between this pair of atomsL1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=8313 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=water SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.2 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label L1 calculates the following quantities:
 Quantity   
 Description  
L1.value
the value of the coordinationL2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=8314 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=water SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.2 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label L2 calculates the following quantities:
 Quantity   
 Description  
L2.value
the value of the coordinationL3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=8315 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=water SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.2 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label L3 calculates the following quantities:
 Quantity   
 Description  
L3.value
the value of the coordinationL4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=8316 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=water SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.2 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label L4 calculates the following quantities:
 Quantity   
 Description  
L4.value
the value of the coordinationL5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=8317 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=water SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.2 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label L5 calculates the following quantities:
 Quantity   
 Description  
L5.value
the value of the coordinationL6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=8318 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=water SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.2 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label L6 calculates the following quantities:
 Quantity   
 Description  
L6.value
the value of the coordinationL7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=8319 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=water SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.2 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10

# Normalize the descriptors for water. Means were obtained from regular 10ns simulation (EQ)
The COORDINATION action with label L7 calculates the following quantities:
 Quantity   
 Description  
L7.value
the value of the coordinationd_w1: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=L1 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d_w1 calculates the following quantities:
 Quantity   
 Description  
d_w1.value
an arbitrary functiond_w2: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=L2 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d_w2 calculates the following quantities:
 Quantity   
 Description  
d_w2.value
an arbitrary functiond_w3: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=L3 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d_w3 calculates the following quantities:
 Quantity   
 Description  
d_w3.value
an arbitrary functiond_w4: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=L4 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d_w4 calculates the following quantities:
 Quantity   
 Description  
d_w4.value
an arbitrary functiond_w5: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=L5 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d_w5 calculates the following quantities:
 Quantity   
 Description  
d_w5.value
an arbitrary functiond_w6: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=L6 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# COM of each A B C ring in QUE
The MATHEVAL action with label d_w6 calculates the following quantities:
 Quantity   
 Description  
d_w6.value
an arbitrary functionCOM_rA: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=8298-8303
The COM action with label COM_rA calculates somethingCOM_rB: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=8307-8312
The COM action with label COM_rB calculates somethingCOM_rC: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=8301,8302,8304-8306,8313

# Some selected key C alpha atoms for each site
# Site 2 (Site B) - Lys43, Phe87, Pro331
The COM action with label COM_rC calculates somethingB_ca1: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=687
The GROUP action with label B_ca1 calculates somethingB_ca2: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1370
The GROUP action with label B_ca2 calculates somethingB_ca3: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=5308

# Descriptors - distances between ring COMs and CA atoms
The GROUP action with label B_ca3 calculates somethingd_rA_b1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_rA,B_ca1
The DISTANCE action with label d_rA_b1 calculates the following quantities:
 Quantity   
 Description  
d_rA_b1.value
the DISTANCE between this pair of atomsd_rA_b2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_rA,B_ca2
The DISTANCE action with label d_rA_b2 calculates the following quantities:
 Quantity   
 Description  
d_rA_b2.value
the DISTANCE between this pair of atomsd_rA_b3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_rA,B_ca3
The DISTANCE action with label d_rA_b3 calculates the following quantities:
 Quantity   
 Description  
d_rA_b3.value
the DISTANCE between this pair of atomsd_rB_b1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_rB,B_ca1
The DISTANCE action with label d_rB_b1 calculates the following quantities:
 Quantity   
 Description  
d_rB_b1.value
the DISTANCE between this pair of atomsd_rB_b2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_rB,B_ca2
The DISTANCE action with label d_rB_b2 calculates the following quantities:
 Quantity   
 Description  
d_rB_b2.value
the DISTANCE between this pair of atomsd_rB_b3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_rB,B_ca3
The DISTANCE action with label d_rB_b3 calculates the following quantities:
 Quantity   
 Description  
d_rB_b3.value
the DISTANCE between this pair of atomsd_rC_b1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_rC,B_ca1
The DISTANCE action with label d_rC_b1 calculates the following quantities:
 Quantity   
 Description  
d_rC_b1.value
the DISTANCE between this pair of atomsd_rC_b2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_rC,B_ca2
The DISTANCE action with label d_rC_b2 calculates the following quantities:
 Quantity   
 Description  
d_rC_b2.value
the DISTANCE between this pair of atomsd_rC_b3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_rC,B_ca3

# --- (3) FUNNEL ---

# Define funnel and walls
The DISTANCE action with label d_rC_b3 calculates the following quantities:
 Quantity   
 Description  
d_rC_b3.value
the DISTANCE between this pair of atomslig: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=8298-8329 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label lig calculates somethingfps: FUNNEL_PSFUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. More details LIGANDThis MUST be a single atom, normally the COM of the ligand=lig REFERENCEa file in pdb format containing the structure you would like to align=../input_structure/6NUC_QUE_reference.pdb ANCHORClosest protein atom to the ligand, picked to avoid pbc problems during the simulation=anchor_atom POINTS6 values defining x, y, and z of the 2 points used to construct the line=3.577,5.841,5.433,6.392,8.482,7.645 NOPBC ignore the periodic boundary conditions when calculating distances
The FUNNEL_PS action with label fps calculates the following quantities:
 Quantity   
 Description  
fps.lp
the position along the funnel line
fps.ld
the distance from the funnel lineFUNNELCalculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. More details ARGthe labels of the scalars on which the bias will act=fps.lp,fps.ld ZCC switching point between cylinder and cone=2.0 ALPHAangle to change the width of the cone section=0.6 RCYLradius of the cylindrical section=0.1 MINSminimum value assumed by fps=-0.5 MAXS maximum value assumed by fps=5.0 KAPPAconstant to be used for the funnel-shape restraint potential=10000 NBINSnumber of bins along fps=500 NBINZnumber of bins along fps=500 FILEname of the Funnel potential file=BIAS LABELa label for the action so that its output can be referenced in the input to other actions=funnel
The FUNNEL action with label funnel calculates the following quantities:
 Quantity   
 Description  
funnel.bias
the instantaneous value of the bias potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=fps.lp ATthe positions of the wall=-0.2 KAPPAthe force constant for the wall=10000 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=lwall
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=fps.lp ATthe positions of the wall=4.5 KAPPAthe force constant for the wall=10000 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall

# --- (4) OTHER QUANTITIES ---

# Keep the protein stable
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialrmsd: RMSDCalculate the RMSD with respect to a reference structure. More details  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../input_structure/6NUC_QUE_reference.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
The RMSD action with label rmsd calculates the following quantities:
 Quantity   
 Description  
rmsd.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd ATthe positions of the wall=0.3 KAPPAthe force constant for the wall=10000 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=rmsdwall

# --- (5) METADYNAMICS ----
# Compute DeepTICA CV
The UPPER_WALLS action with label rmsdwall calculates the following quantities:
 Quantity   
 Description  
rmsdwall.bias
the instantaneous value of the bias potential
rmsdwall.force2
the instantaneous value of the squared force due to this bias potentialdeep: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=../deeptica_models/model_site2.ptc ARGthe labels of the values from which the function is calculated=d_L_B,d_w1,d_w2,d_w3,d_w4,d_w5,d_w6,d_rA_b1,d_rA_b2,d_rA_b3,d_rB_b1,d_rB_b2,d_rB_b3,d_rC_b1,d_rC_b2,d_rC_b3

# Well-tempered metadynamics using DeepTICA CV and funnel projection
The PYTORCH_MODEL action with label deep calculates the following quantities:
 Quantity   
 Description  
deep.node
Model outputsmetad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=deep.node-0,fps.lp PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.2 SIGMAthe widths of the Gaussian hills=0.1,0.1 BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 FILE a file in which the list of added hills is stored=HILLS GRID_MINthe lower bounds for the grid=-60.0,-1.0 GRID_MAXthe upper bounds for the grid=60.0,5.5 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.01,0.01 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor c(t)PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR FMT the format that should be used to output real numbers=%8.4f