Project ID: plumID:24.017
Source: BRD4/MetaDynamics/lig11/run3/plumed.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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=../whole.pdb
The MOLINFO action with label calculates somethingproteinThe GROUP action with label protein calculates the following quantities:| Quantity | Type | Description |
| protein | atoms | indices of atoms specified in GROUP |
: 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=1-2121
ligandThe GROUP action with label ligand calculates the following quantities:| Quantity | Type | Description |
| ligand | atoms | indices of atoms specified in GROUP |
: 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=2122-2147
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=protein ENTITY1the atoms that make up a molecule that you wish to align=ligand
WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=ligand AROUNDreference atoms=1586 GROUPBY group atoms so as not to break molecules=26
ligThe COM action with label lig calculates the following quantities:| Quantity | Type | Description |
| lig | atoms | virtual atom calculated by COM action |
: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=ligand
p0The COM action with label p0 calculates the following quantities:| Quantity | Type | Description |
| p0 | atoms | virtual atom calculated by COM action |
: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1105,1461,1473,1521
p1The COM action with label p1 calculates the following quantities:| Quantity | Type | Description |
| p1 | atoms | virtual atom calculated by COM action |
: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=824,846,1122,1586,1739,1774
WOThe GROUP action with label WO calculates the following quantities:| Quantity | Type | Description |
| WO | atoms | indices of atoms specified in GROUP |
: 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=2148-30326:3
G1The GROUP action with label G1 calculates the following quantities:| Quantity | Type | Description |
| G1 | atoms | indices of atoms specified in GROUP |
: 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=2144
G2The GROUP action with label G2 calculates the following quantities:| Quantity | Type | Description |
| G2 | atoms | indices of atoms specified in GROUP |
: 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=2132
G3The GROUP action with label G3 calculates the following quantities:| Quantity | Type | Description |
| G3 | atoms | indices of atoms specified in GROUP |
: 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=2134
NG1The COORDINATION action with label NG1 calculates the following quantities:| Quantity | Type | Description |
| NG1 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=G1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NG2The COORDINATION action with label NG2 calculates the following quantities:| Quantity | Type | Description |
| NG2 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=G2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NG3The COORDINATION action with label NG3 calculates the following quantities:| Quantity | Type | Description |
| NG3 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=G3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
P1The GROUP action with label P1 calculates the following quantities:| Quantity | Type | Description |
| P1 | atoms | indices of atoms specified in GROUP |
: 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=1590
P2The GROUP action with label P2 calculates the following quantities:| Quantity | Type | Description |
| P2 | atoms | indices of atoms specified in GROUP |
: 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=1647
P3The GROUP action with label P3 calculates the following quantities:| Quantity | Type | Description |
| P3 | atoms | indices of atoms specified in GROUP |
: 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=934
P4The GROUP action with label P4 calculates the following quantities:| Quantity | Type | Description |
| P4 | atoms | indices of atoms specified in GROUP |
: 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=1528
NP1The COORDINATION action with label NP1 calculates the following quantities:| Quantity | Type | Description |
| NP1 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=P1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NP2The COORDINATION action with label NP2 calculates the following quantities:| Quantity | Type | Description |
| NP2 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=P2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NP3The COORDINATION action with label NP3 calculates the following quantities:| Quantity | Type | Description |
| NP3 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=P3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NP4The COORDINATION action with label NP4 calculates the following quantities:| Quantity | Type | Description |
| NP4 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=P4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO 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 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
ppThe PROJECTION_ON_AXIS action with label pp calculates the following quantities:| Quantity | Type | Description |
| pp.proj | scalar | The value of the projection along the axis |
| pp.ext | scalar | The value of the extension from the axis |
: PROJECTION_ON_AXISCalculate a position based on the projection along and extension from a defined axis. More details AXIS_ATOMSThe atoms that define the direction of the axis of interest=p0,p1 ATOMThe atom whose position we want to project on the axis of interest=lig
rmsd_protCAThe RMSD action with label rmsd_protCA calculates the following quantities:| Quantity | Type | Description |
| rmsd_protCA | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_protCA: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
uwall_rmsd_protCAThe UPPER_WALLS action with label uwall_rmsd_protCA calculates the following quantities:| Quantity | Type | Description |
| uwall_rmsd_protCA.bias | scalar | the instantaneous value of the bias potential |
| uwall_rmsd_protCA.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_protCA ATthe positions of the wall=0.4 KAPPAthe force constant for the wall=200000
rmsd_pocket_1The RMSD action with label rmsd_pocket_1 calculates the following quantities:| Quantity | Type | Description |
| rmsd_pocket_1 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_1.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_pocket_1: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_1.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
uwall_rmsd_pocket_1The UPPER_WALLS action with label uwall_rmsd_pocket_1 calculates the following quantities:| Quantity | Type | Description |
| uwall_rmsd_pocket_1.bias | scalar | the instantaneous value of the bias potential |
| uwall_rmsd_pocket_1.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_pocket_1 ATthe positions of the wall=0.3 KAPPAthe force constant for the wall=200000
rmsd_pocket_2The RMSD action with label rmsd_pocket_2 calculates the following quantities:| Quantity | Type | Description |
| rmsd_pocket_2 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_pocket_2: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
uwall_rmsd_pocket_2The UPPER_WALLS action with label uwall_rmsd_pocket_2 calculates the following quantities:| Quantity | Type | Description |
| uwall_rmsd_pocket_2.bias | scalar | the instantaneous value of the bias potential |
| uwall_rmsd_pocket_2.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_pocket_2 ATthe positions of the wall=0.25 KAPPAthe force constant for the wall=200000
rmsd_pocket_3The RMSD action with label rmsd_pocket_3 calculates the following quantities:| Quantity | Type | Description |
| rmsd_pocket_3 | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_3.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_pocket_3: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_3.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
uwall_rmsd_pocket_3The UPPER_WALLS action with label uwall_rmsd_pocket_3 calculates the following quantities:| Quantity | Type | Description |
| uwall_rmsd_pocket_3.bias | scalar | the instantaneous value of the bias potential |
| uwall_rmsd_pocket_3.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_pocket_3 ATthe positions of the wall=0.25 KAPPAthe force constant for the wall=200000
rmsd_tailThe RMSD action with label rmsd_tail calculates the following quantities:| Quantity | Type | Description |
| rmsd_tail | scalar | the RMSD between the instantaneous structure and the reference structure that was input |
: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_tail.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_tail: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_tail.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
uwall_rmsd_tailThe UPPER_WALLS action with label uwall_rmsd_tail calculates the following quantities:| Quantity | Type | Description |
| uwall_rmsd_tail.bias | scalar | the instantaneous value of the bias potential |
| uwall_rmsd_tail.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_tail ATthe positions of the wall=0.35 KAPPAthe force constant for the wall=200000
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=../cmap.dat
# INCLUDE FILE=../cmap.dat
The INCLUDE action with label ../cmap.dat calculates somethingCONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=1665,2133 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=699,2130 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=1747,2125 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1801,2147 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=cmapThe CONTACTMAP action with label cmap calculates the following quantities:| Quantity | Type | Description |
| cmap | scalar | the sum of all the switching function on all the distances |
SUM calculate the sum of all the contacts in the input
... CONTACTMAP
CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=1665,2133 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}
ATOMS2the atoms involved in each of the contacts you wish to calculate=699,2130 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}
ATOMS3the atoms involved in each of the contacts you wish to calculate=1747,2125 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1801,2147 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}
LABELa label for the action so that its output can be referenced in the input to other actions=cmappaThe CONTACTMAP action with label cmappa calculates the following quantities:| Quantity | Type | Description |
| cmappa.contact-1 | scalar | By not using SUM or CMDIST each contact will be stored in a component This is the 1th of these quantities |
| cmappa.contact-2 | scalar | By not using SUM or CMDIST each contact will be stored in a component This is the 2th of these quantities |
| cmappa.contact-3 | scalar | By not using SUM or CMDIST each contact will be stored in a component This is the 3th of these quantities |
| cmappa.contact-4 | scalar | By not using SUM or CMDIST each contact will be stored in a component This is the 4th of these quantities |
... CONTACTMAP
# --- End of included input ---
lig_torsion1The TORSION action with label lig_torsion1 calculates the following quantities:| Quantity | Type | Description |
| lig_torsion1 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2131,2128,2126,2125
s_centThe CONSTANT action with label s_cent calculates the following quantities:| Quantity | Type | Description |
| s_cent | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=2.6
s_cent: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=2.6
beta_centThe CONSTANT action with label beta_cent calculates the following quantities:| Quantity | Type | Description |
| beta_cent | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.8
beta_cent: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.8
wall_widthThe CONSTANT action with label wall_width calculates the following quantities:| Quantity | Type | Description |
| wall_width | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.1
wall_width: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.1
wall_bufferThe CONSTANT action with label wall_buffer calculates the following quantities:| Quantity | Type | Description |
| wall_buffer | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.25
wall_buffer: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.25
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:| Quantity | Type | Description |
| lwall.bias | scalar | the instantaneous value of the bias potential |
| lwall.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.proj ATthe positions of the wall=1.2 KAPPAthe force constant for the wall=2000
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:| Quantity | Type | Description |
| uwall.bias | scalar | the instantaneous value of the bias potential |
| uwall.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.proj ATthe positions of the wall=3.3 KAPPAthe force constant for the wall=2000
MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=wall_centerThe MATHEVAL action with label wall_center calculates the following quantities:| Quantity | Type | Description |
| wall_center | scalar | an arbitrary function |
ARGthe values input to this function=pp.proj,s_cent,beta_cent,wall_width,wall_buffer
VARthe names to give each of the arguments in the function=s,sc,b,h,f
FUNCthe function you wish to evaluate=h*(1./(1.+exp(b*(s-sc))))+f
PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL
scalingThe CONSTANT action with label scaling calculates the following quantities:| Quantity | Type | Description |
| scaling | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1.0
scaling: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1.0 NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
springThe CONSTANT action with label spring calculates the following quantities:| Quantity | Type | Description |
| spring | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=10000.0
spring: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=10000.0 NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=wall_biasThe MATHEVAL action with label wall_bias calculates the following quantities:| Quantity | Type | Description |
| wall_bias | scalar | an arbitrary function |
ARGthe values input to this function=pp.ext,spring,wall_center,scaling
VARthe names to give each of the arguments in the function=z,k,zc,sf
FUNCthe function you wish to evaluate=step(z-zc)*k*(z-zc)*(z-zc)/(sf*sf)
PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL
finalbiasThe BIASVALUE action with label finalbias calculates the following quantities:| Quantity | Type | Description |
| finalbias.bias | scalar | the instantaneous value of the bias potential |
| finalbias.wall_bias_bias | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named wall_bias |
: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=wall_bias
eneThe ENERGY action with label ene calculates the following quantities:| Quantity | Type | Description |
| ene | scalar | the internal energy |
: ENERGYCalculate the total potential energy of the simulation box. More details
ecvThe ECV_MULTITHERMAL action with label ecv calculates the following quantities:| Quantity | Type | Description |
| ecv.ene | scalar | the value of the argument named ene |
: ECV_MULTITHERMALExpand a simulation to sample multiple temperatures simultaneously. This action has hidden defaults. More details ARGthe label of the internal energy of the system=ene TEMP_MAXthe maximum of the temperature range=310
ecv: ECV_MULTITHERMALExpand a simulation to sample multiple temperatures simultaneously. This action uses the defaults shown here. More details ARGthe label of the internal energy of the system=ene TEMP_MAXthe maximum of the temperature range=310 TEMP temperature=-1
opesXThe OPES_EXPANDED action with label opesX calculates the following quantities:| Quantity | Type | Description |
| opesX.bias | scalar | the instantaneous value of the bias potential |
: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action has hidden defaults. More details ARGthe label of the ECVs that define the expansion=ecv.* FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DeltaFs.data PACEhow often the bias is updated=2000
opesX: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action uses the defaults shown here. More details ARGthe label of the ECVs that define the expansion=ecv.* FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DeltaFs.data PACEhow often the bias is updated=2000 OBSERVATION_STEPS number of unbiased initial PACE steps to collect statistics for initialization=100 PRINT_STRIDE stride for printing to DELTAFS file, in units of PACE=100
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opesThe OPES_METAD_EXPLORE action with label opes calculates the following quantities:| Quantity | Type | Description |
| opes.bias | scalar | the instantaneous value of the bias potential |
| opes.rct | scalar | estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting |
| opes.zed | scalar | estimate of Z_n. should become flat once no new CV-space region is explored |
| opes.neff | scalar | effective sample size |
| opes.nker | scalar | total number of compressed kernels used to represent the bias |
ARGthe labels of the scalars on which the bias will act=pp.proj,cmap
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.05,0.3
FILE a file in which the list of all deposited kernels is stored=Kernels.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
PACEthe frequency for kernel deposition=20000
BARRIERthe free energy barrier to be overcome=30
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opes
ARGthe labels of the scalars on which the bias will act=pp.proj,cmap
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.05,0.3
FILE a file in which the list of all deposited kernels is stored=Kernels.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
PACEthe frequency for kernel deposition=20000
BARRIERthe free energy barrier to be overcome=30
TEMP temperature=-1 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opesNP1The OPES_METAD_EXPLORE action with label opesNP1 calculates the following quantities:| Quantity | Type | Description |
| opesNP1.bias | scalar | the instantaneous value of the bias potential |
| opesNP1.rct | scalar | estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting |
| opesNP1.zed | scalar | estimate of Z_n. should become flat once no new CV-space region is explored |
| opesNP1.neff | scalar | effective sample size |
| opesNP1.nker | scalar | total number of compressed kernels used to represent the bias |
ARGthe labels of the scalars on which the bias will act=NP1,lig_torsion1
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.2,0.2
FILE a file in which the list of all deposited kernels is stored=KernelsNP1.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP1
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP1
PACEthe frequency for kernel deposition=40000
BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opesNP1
ARGthe labels of the scalars on which the bias will act=NP1,lig_torsion1
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.2,0.2
FILE a file in which the list of all deposited kernels is stored=KernelsNP1.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP1
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP1
PACEthe frequency for kernel deposition=40000
BARRIERthe free energy barrier to be overcome=3
TEMP temperature=-1 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opesNP2The OPES_METAD_EXPLORE action with label opesNP2 calculates the following quantities:| Quantity | Type | Description |
| opesNP2.bias | scalar | the instantaneous value of the bias potential |
| opesNP2.rct | scalar | estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting |
| opesNP2.zed | scalar | estimate of Z_n. should become flat once no new CV-space region is explored |
| opesNP2.neff | scalar | effective sample size |
| opesNP2.nker | scalar | total number of compressed kernels used to represent the bias |
ARGthe labels of the scalars on which the bias will act=NP2,lig_torsion1
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.2,0.2
FILE a file in which the list of all deposited kernels is stored=KernelsNP2.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP2
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP2
PACEthe frequency for kernel deposition=40000
BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opesNP2
ARGthe labels of the scalars on which the bias will act=NP2,lig_torsion1
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.2,0.2
FILE a file in which the list of all deposited kernels is stored=KernelsNP2.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP2
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP2
PACEthe frequency for kernel deposition=40000
BARRIERthe free energy barrier to be overcome=3
TEMP temperature=-1 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opesNP3The OPES_METAD_EXPLORE action with label opesNP3 calculates the following quantities:| Quantity | Type | Description |
| opesNP3.bias | scalar | the instantaneous value of the bias potential |
| opesNP3.rct | scalar | estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting |
| opesNP3.zed | scalar | estimate of Z_n. should become flat once no new CV-space region is explored |
| opesNP3.neff | scalar | effective sample size |
| opesNP3.nker | scalar | total number of compressed kernels used to represent the bias |
ARGthe labels of the scalars on which the bias will act=NP3,lig_torsion1
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.1,0.2
FILE a file in which the list of all deposited kernels is stored=KernelsNP3.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP3
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP3
PACEthe frequency for kernel deposition=40000
BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opesNP3
ARGthe labels of the scalars on which the bias will act=NP3,lig_torsion1
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.1,0.2
FILE a file in which the list of all deposited kernels is stored=KernelsNP3.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP3
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP3
PACEthe frequency for kernel deposition=40000
BARRIERthe free energy barrier to be overcome=3
TEMP temperature=-1 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD_EXPLORE
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f
