Project ID: plumID:22.009
Source: plumed.dat
Originally used with PLUMED version: 2.5
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
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=0.001
The UNITS action with label 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=1-432 ENTITY1the atoms that make up a molecule that you wish to align=433-442 ENTITY2the atoms that make up a molecule that you wish to align=449-451 ENTITY3the atoms that make up a molecule that you wish to align=452-454 ENTITY4the atoms that make up a molecule that you wish to align=455-457 ENTITY5the atoms that make up a molecule that you wish to align=458-460 ENTITY6the atoms that make up a molecule that you wish to align=461-463 ENTITY7the atoms that make up a molecule that you wish to align=464-466 ENTITY8the atoms that make up a molecule that you wish to align=467-469 ENTITY9the atoms that make up a molecule that you wish to align=470-472
FIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=heavy_atoms.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_calThe RMSD action with label rmsd_cal calculates the following quantities: Quantity | Type | Description |
rmsd_cal | 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=heavy_atoms_cal.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_cal: 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=heavy_atoms_cal.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
rmsd_watThe RMSD action with label rmsd_wat calculates the following quantities: Quantity | Type | Description |
rmsd_wat | 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=heavy_atoms_wat.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_wat: 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=heavy_atoms_wat.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
rmsd_subThe RMSD action with label rmsd_sub calculates the following quantities: Quantity | Type | Description |
rmsd_sub | 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=heavy_atoms_sub.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_sub: 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=heavy_atoms_sub.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
rmsd_allThe RMSD action with label rmsd_all calculates the following quantities: Quantity | Type | Description |
rmsd_all | 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=heavy_atoms_npt_sel.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_all: 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=heavy_atoms_npt_sel.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
hThe GROUP action with label h calculates the following quantities: Quantity | Type | Description |
h | 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=473,484,485,30,102,123,33,2,120,481,482
o_phThe GROUP action with label o_ph calculates the following quantities: Quantity | Type | Description |
o_ph | 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=29,101,122,32,119,1
o_w1The GROUP action with label o_w1 calculates the following quantities: Quantity | Type | Description |
o_w1 | 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=483
o_w2The GROUP action with label o_w2 calculates the following quantities: Quantity | Type | Description |
o_w2 | 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=480
o_meThe GROUP action with label o_me calculates the following quantities: Quantity | Type | Description |
o_me | 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=472
clThe GROUP action with label cl calculates the following quantities: Quantity | Type | Description |
cl | 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=455
glyThe GROUP action with label gly calculates the following quantities: Quantity | Type | Description |
gly | 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=448,447,454,457,458,438,437,440,441,463
d_cloThe DISTANCE action with label d_clo calculates the following quantities: Quantity | Type | Description |
d_clo | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=455,480
d_ohoThe DISTANCE action with label d_oho calculates the following quantities: Quantity | Type | Description |
d_oho | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=472,483
d_oclThe DISTANCE action with label d_ocl calculates the following quantities: Quantity | Type | Description |
d_ocl | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=472,454
d_clcThe DISTANCE action with label d_clc calculates the following quantities: Quantity | Type | Description |
d_clc | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=455,454
d_mecThe DISTANCE action with label d_mec calculates the following quantities: Quantity | Type | Description |
d_mec | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=472,454
d_hgcThe DISTANCE action with label d_hgc calculates the following quantities: Quantity | Type | Description |
d_hgc | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=456,454
d_hgc2The DISTANCE action with label d_hgc2 calculates the following quantities: Quantity | Type | Description |
d_hgc2 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=459,458
d_w2ph1The DISTANCE action with label d_w2ph1 calculates the following quantities: Quantity | Type | Description |
d_w2ph1 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=o_w2,1
d_w2ph2The DISTANCE action with label d_w2ph2 calculates the following quantities: Quantity | Type | Description |
d_w2ph2 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=o_w2,119
b_cloThe BRIDGE action with label b_clo calculates the following quantities: Quantity | Type | Description |
b_clo | scalar | the number of bridging atoms between the two groups |
: BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=cl GROUPB=o_w2 SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=1.5}
# b_clo: BRIDGE BRIDGING_ATOMS=h GROUPA=cl GROUPB=o_w2 SWITCH={RATIONAL R_0=1.5}
b_clo_matThe BRIDGE_MATRIX action with label b_clo_mat calculates the following quantities: Quantity | Type | Description |
b_clo_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure More details SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=1.5} BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=cl GROUPB=o_w2
b_cloThe SUM action with label b_clo calculates the following quantities: Quantity | Type | Description |
b_clo | scalar | the sum of all the elements in the input matrix |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=b_clo_mat PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- b_ohoThe BRIDGE action with label b_oho calculates the following quantities: Quantity | Type | Description |
b_oho | scalar | the number of bridging atoms between the two groups |
: BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=o_me GROUPB=o_w1 SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=1.5}
# b_oho: BRIDGE BRIDGING_ATOMS=h GROUPA=o_me GROUPB=o_w1 SWITCH={RATIONAL R_0=1.5}
b_oho_matThe BRIDGE_MATRIX action with label b_oho_mat calculates the following quantities: Quantity | Type | Description |
b_oho_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure More details SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=1.5} BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=o_me GROUPB=o_w1
b_ohoThe SUM action with label b_oho calculates the following quantities: Quantity | Type | Description |
b_oho | scalar | the sum of all the elements in the input matrix |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=b_oho_mat PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- b_clmThe BRIDGE action with label b_clm calculates the following quantities: Quantity | Type | Description |
b_clm | scalar | the number of bridging atoms between the two groups |
: BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=cl GROUPB=o_w1 SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=2.0}
# b_clm: BRIDGE BRIDGING_ATOMS=h GROUPA=cl GROUPB=o_w1 SWITCH={RATIONAL R_0=2.0}
b_clm_matThe BRIDGE_MATRIX action with label b_clm_mat calculates the following quantities: Quantity | Type | Description |
b_clm_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure More details SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=2.0} BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=cl GROUPB=o_w1
b_clmThe SUM action with label b_clm calculates the following quantities: Quantity | Type | Description |
b_clm | scalar | the sum of all the elements in the input matrix |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=b_clm_mat PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- b_clgThe BRIDGE action with label b_clg calculates the following quantities: Quantity | Type | Description |
b_clg | scalar | the number of bridging atoms between the two groups |
: BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=cl GROUPB=gly SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=2.0}
# b_clg: BRIDGE BRIDGING_ATOMS=h GROUPA=cl GROUPB=gly SWITCH={RATIONAL R_0=2.0}
b_clg_matThe BRIDGE_MATRIX action with label b_clg_mat calculates the following quantities: Quantity | Type | Description |
b_clg_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure More details SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=2.0} BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=cl GROUPB=gly
b_clgThe SUM action with label b_clg calculates the following quantities: Quantity | Type | Description |
b_clg | scalar | the sum of all the elements in the input matrix |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=b_clg_mat PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- b_clpThe BRIDGE action with label b_clp calculates the following quantities: Quantity | Type | Description |
b_clp | scalar | the number of bridging atoms between the two groups |
: BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=cl GROUPB=o_ph SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=2.0}
# b_clp: BRIDGE BRIDGING_ATOMS=h GROUPA=cl GROUPB=o_ph SWITCH={RATIONAL R_0=2.0}
b_clp_matThe BRIDGE_MATRIX action with label b_clp_mat calculates the following quantities: Quantity | Type | Description |
b_clp_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: BRIDGE_MATRIXCalculate the number of atoms that bridge two parts of a structure More details SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=2.0} BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=cl GROUPB=o_ph
b_clpThe SUM action with label b_clp calculates the following quantities: Quantity | Type | Description |
b_clp | scalar | the sum of all the elements in the input matrix |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=b_clp_mat PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
c_o_w1hThe COORDINATION action with label c_o_w1h calculates the following quantities: Quantity | Type | Description |
c_o_w1h | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=o_w1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=h R_0The r_0 parameter of the switching function=1.5
c_o_w1h: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=o_w1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=h R_0The r_0 parameter of the switching function=1.5 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
c_o_mehThe COORDINATION action with label c_o_meh calculates the following quantities: Quantity | Type | Description |
c_o_meh | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=o_me GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=h R_0The r_0 parameter of the switching function=1.5
c_o_meh: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=o_me GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=h R_0The r_0 parameter of the switching function=1.5 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
c_h_clThe COORDINATION action with label c_h_cl calculates the following quantities: Quantity | Type | Description |
c_h_cl | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=cl GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=h R_0The r_0 parameter of the switching function=2.0
c_h_cl: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=cl GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=h R_0The r_0 parameter of the switching function=2.0 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
diffThe COMBINE action with label diff calculates the following quantities: Quantity | Type | Description |
diff | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d_clc,d_mec COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
prodThe MATHEVAL action with label prod calculates the following quantities: Quantity | Type | Description |
prod | scalar | an arbitrary function |
: 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=c_o_w1h,c_o_meh FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
aThe ANGLE action with label a calculates the following quantities: Quantity | Type | Description |
a | scalar | the ANGLE involving these atoms |
: ANGLECalculate an angle. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=455,454,472
a1The ANGLE action with label a1 calculates the following quantities: Quantity | Type | Description |
a1 | scalar | the ANGLE involving these atoms |
: ANGLECalculate an angle. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=480,455,454
a2The ANGLE action with label a2 calculates the following quantities: Quantity | Type | Description |
a2 | scalar | the ANGLE involving these atoms |
: ANGLECalculate an angle. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=454,472,483
dch1The DISTANCES action with label dch1 calculates the following quantities: Quantity | Type | Description |
dch1 | vector | the DISTANCES between the each pair of atoms that were specified |
dch1_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=464 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=465,466,467 MEAN calculate the mean of all the quantities
# dch1: DISTANCES GROUPA=464 GROUPB=465,466,467 MEAN
dch1The DISTANCE action with label dch1 calculates the following quantities: Quantity | Type | Description |
dch1 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=464,465 ATOMS2the pair of atom that we are calculating the distance between=464,466 ATOMS3the pair of atom that we are calculating the distance between=464,467
dch1_meanThe MEAN action with label dch1_mean calculates the following quantities: Quantity | Type | Description |
dch1_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dch1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dch2The DISTANCES action with label dch2 calculates the following quantities: Quantity | Type | Description |
dch2 | vector | the DISTANCES between the each pair of atoms that were specified |
dch2_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=460 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=461,462 MEAN calculate the mean of all the quantities
# dch2: DISTANCES GROUPA=460 GROUPB=461,462 MEAN
dch2The DISTANCE action with label dch2 calculates the following quantities: Quantity | Type | Description |
dch2 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=460,461 ATOMS2the pair of atom that we are calculating the distance between=460,462
dch2_meanThe MEAN action with label dch2_mean calculates the following quantities: Quantity | Type | Description |
dch2_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dch2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dch3The DISTANCES action with label dch3 calculates the following quantities: Quantity | Type | Description |
dch3 | vector | the DISTANCES between the each pair of atoms that were specified |
dch3_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=433 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=435,436,434 MEAN calculate the mean of all the quantities
# dch3: DISTANCES GROUPA=433 GROUPB=435,436,434 MEAN
dch3The DISTANCE action with label dch3 calculates the following quantities: Quantity | Type | Description |
dch3 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=433,435 ATOMS2the pair of atom that we are calculating the distance between=433,436 ATOMS3the pair of atom that we are calculating the distance between=433,434
dch3_meanThe MEAN action with label dch3_mean calculates the following quantities: Quantity | Type | Description |
dch3_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dch3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dch4The DISTANCES action with label dch4 calculates the following quantities: Quantity | Type | Description |
dch4 | vector | the DISTANCES between the each pair of atoms that were specified |
dch4_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=438 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=439 MEAN calculate the mean of all the quantities
# dch4: DISTANCES GROUPA=438 GROUPB=439 MEAN
dch4The DISTANCE action with label dch4 calculates the following quantities: Quantity | Type | Description |
dch4 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=438,439
dch4_meanThe MEAN action with label dch4_mean calculates the following quantities: Quantity | Type | Description |
dch4_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dch4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dch5The DISTANCES action with label dch5 calculates the following quantities: Quantity | Type | Description |
dch5 | vector | the DISTANCES between the each pair of atoms that were specified |
dch5_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=442 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=445,443,444 MEAN calculate the mean of all the quantities
# dch5: DISTANCES GROUPA=442 GROUPB=445,443,444 MEAN
dch5The DISTANCE action with label dch5 calculates the following quantities: Quantity | Type | Description |
dch5 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=442,445 ATOMS2the pair of atom that we are calculating the distance between=442,443 ATOMS3the pair of atom that we are calculating the distance between=442,444
dch5_meanThe MEAN action with label dch5_mean calculates the following quantities: Quantity | Type | Description |
dch5_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dch5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dch6The DISTANCES action with label dch6 calculates the following quantities: Quantity | Type | Description |
dch6 | vector | the DISTANCES between the each pair of atoms that were specified |
dch6_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=454 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=456 MEAN calculate the mean of all the quantities
# dch6: DISTANCES GROUPA=454 GROUPB=456 MEAN
dch6The DISTANCE action with label dch6 calculates the following quantities: Quantity | Type | Description |
dch6 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=454,456
dch6_meanThe MEAN action with label dch6_mean calculates the following quantities: Quantity | Type | Description |
dch6_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dch6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dch7The DISTANCES action with label dch7 calculates the following quantities: Quantity | Type | Description |
dch7 | vector | the DISTANCES between the each pair of atoms that were specified |
dch7_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=447 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=453 MEAN calculate the mean of all the quantities
# dch7: DISTANCES GROUPA=447 GROUPB=453 MEAN
dch7The DISTANCE action with label dch7 calculates the following quantities: Quantity | Type | Description |
dch7 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=447,453
dch7_meanThe MEAN action with label dch7_mean calculates the following quantities: Quantity | Type | Description |
dch7_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dch7 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dch8The DISTANCES action with label dch8 calculates the following quantities: Quantity | Type | Description |
dch8 | vector | the DISTANCES between the each pair of atoms that were specified |
dch8_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=449 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=450,451,452 MEAN calculate the mean of all the quantities
# dch8: DISTANCES GROUPA=449 GROUPB=450,451,452 MEAN
dch8The DISTANCE action with label dch8 calculates the following quantities: Quantity | Type | Description |
dch8 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=449,450 ATOMS2the pair of atom that we are calculating the distance between=449,451 ATOMS3the pair of atom that we are calculating the distance between=449,452
dch8_meanThe MEAN action with label dch8_mean calculates the following quantities: Quantity | Type | Description |
dch8_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dch8 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
dco1The DISTANCES action with label dco1 calculates the following quantities: Quantity | Type | Description |
dco1 | vector | the DISTANCES between the each pair of atoms that were specified |
dco1_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=454,458 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=457 MEAN calculate the mean of all the quantities
# dco1: DISTANCES GROUPA=454,458 GROUPB=457 MEAN
dco1The DISTANCE action with label dco1 calculates the following quantities: Quantity | Type | Description |
dco1 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=454,457 ATOMS2the pair of atom that we are calculating the distance between=458,457
dco1_meanThe MEAN action with label dco1_mean calculates the following quantities: Quantity | Type | Description |
dco1_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dco1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dco2The DISTANCES action with label dco2 calculates the following quantities: Quantity | Type | Description |
dco2 | vector | the DISTANCES between the each pair of atoms that were specified |
dco2_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=464,460 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=463 MEAN calculate the mean of all the quantities
# dco2: DISTANCES GROUPA=464,460 GROUPB=463 MEAN
dco2The DISTANCE action with label dco2 calculates the following quantities: Quantity | Type | Description |
dco2 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=464,463 ATOMS2the pair of atom that we are calculating the distance between=460,463
dco2_meanThe MEAN action with label dco2_mean calculates the following quantities: Quantity | Type | Description |
dco2_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dco2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dco3The DISTANCES action with label dco3 calculates the following quantities: Quantity | Type | Description |
dco3 | vector | the DISTANCES between the each pair of atoms that were specified |
dco3_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=433,438 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=437 MEAN calculate the mean of all the quantities
# dco3: DISTANCES GROUPA=433,438 GROUPB=437 MEAN
dco3The DISTANCE action with label dco3 calculates the following quantities: Quantity | Type | Description |
dco3 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=433,437 ATOMS2the pair of atom that we are calculating the distance between=438,437
dco3_meanThe MEAN action with label dco3_mean calculates the following quantities: Quantity | Type | Description |
dco3_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dco3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dco4The DISTANCES action with label dco4 calculates the following quantities: Quantity | Type | Description |
dco4 | vector | the DISTANCES between the each pair of atoms that were specified |
dco4_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=440,442 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=441 MEAN calculate the mean of all the quantities
# dco4: DISTANCES GROUPA=440,442 GROUPB=441 MEAN
dco4The DISTANCE action with label dco4 calculates the following quantities: Quantity | Type | Description |
dco4 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=440,441 ATOMS2the pair of atom that we are calculating the distance between=442,441
dco4_meanThe MEAN action with label dco4_mean calculates the following quantities: Quantity | Type | Description |
dco4_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dco4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dco5The DISTANCES action with label dco5 calculates the following quantities: Quantity | Type | Description |
dco5 | vector | the DISTANCES between the each pair of atoms that were specified |
dco5_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=447,449 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=448 MEAN calculate the mean of all the quantities
# dco5: DISTANCES GROUPA=447,449 GROUPB=448 MEAN
dco5The DISTANCE action with label dco5 calculates the following quantities: Quantity | Type | Description |
dco5 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance between a pair of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=447,448 ATOMS2the pair of atom that we are calculating the distance between=449,448
dco5_meanThe MEAN action with label dco5_mean calculates the following quantities: Quantity | Type | Description |
dco5_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=dco5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
uwall_1The UPPER_WALLS action with label uwall_1 calculates the following quantities: Quantity | Type | Description |
uwall_1.bias | scalar | the instantaneous value of the bias potential |
uwall_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=d_clo ATthe positions of the wall=2.5 KAPPAthe force constant for the wall=200
uwall_2The UPPER_WALLS action with label uwall_2 calculates the following quantities: Quantity | Type | Description |
uwall_2.bias | scalar | the instantaneous value of the bias potential |
uwall_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=d_oho ATthe positions of the wall=2.5 KAPPAthe force constant for the wall=200
uwall_6The UPPER_WALLS action with label uwall_6 calculates the following quantities: Quantity | Type | Description |
uwall_6.bias | scalar | the instantaneous value of the bias potential |
uwall_6.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_all ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=25000
uwall_7The LOWER_WALLS action with label uwall_7 calculates the following quantities: Quantity | Type | Description |
uwall_7.bias | scalar | the instantaneous value of the bias potential |
uwall_7.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=b_clo ATthe positions of the wall=+0.5 KAPPAthe force constant for the wall=700
uwall_8The LOWER_WALLS action with label uwall_8 calculates the following quantities: Quantity | Type | Description |
uwall_8.bias | scalar | the instantaneous value of the bias potential |
uwall_8.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=b_oho ATthe positions of the wall=+0.5 KAPPAthe force constant for the wall=700
uwall_10The UPPER_WALLS action with label uwall_10 calculates the following quantities: Quantity | Type | Description |
uwall_10.bias | scalar | the instantaneous value of the bias potential |
uwall_10.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=prod ATthe positions of the wall=+2.5 KAPPAthe force constant for the wall=200
uwall_11The LOWER_WALLS action with label uwall_11 calculates the following quantities: Quantity | Type | Description |
uwall_11.bias | scalar | the instantaneous value of the bias potential |
uwall_11.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=prod ATthe positions of the wall=+2.0 KAPPAthe force constant for the wall=150
uwall_12The UPPER_WALLS action with label uwall_12 calculates the following quantities: Quantity | Type | Description |
uwall_12.bias | scalar | the instantaneous value of the bias potential |
uwall_12.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=diff ATthe positions of the wall=+2.5 KAPPAthe force constant for the wall=150
uwall_13The LOWER_WALLS action with label uwall_13 calculates the following quantities: Quantity | Type | Description |
uwall_13.bias | scalar | the instantaneous value of the bias potential |
uwall_13.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=diff ATthe positions of the wall=-2.5 KAPPAthe force constant for the wall=200
uwall_15The UPPER_WALLS action with label uwall_15 calculates the following quantities: Quantity | Type | Description |
uwall_15.bias | scalar | the instantaneous value of the bias potential |
uwall_15.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=c_h_cl ATthe positions of the wall=+1.1 KAPPAthe force constant for the wall=300
uwall_16The UPPER_WALLS action with label uwall_16 calculates the following quantities: Quantity | Type | Description |
uwall_16.bias | scalar | the instantaneous value of the bias potential |
uwall_16.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=b_clm ATthe positions of the wall=+0.0 KAPPAthe force constant for the wall=700
uwall_17The UPPER_WALLS action with label uwall_17 calculates the following quantities: Quantity | Type | Description |
uwall_17.bias | scalar | the instantaneous value of the bias potential |
uwall_17.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=b_clg ATthe positions of the wall=+0.1 KAPPAthe force constant for the wall=700
uwall_18The UPPER_WALLS action with label uwall_18 calculates the following quantities: Quantity | Type | Description |
uwall_18.bias | scalar | the instantaneous value of the bias potential |
uwall_18.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=b_clp ATthe positions of the wall=+0.1 KAPPAthe force constant for the wall=700
uwall_19The UPPER_WALLS action with label uwall_19 calculates the following quantities: Quantity | Type | Description |
uwall_19.bias | scalar | the instantaneous value of the bias potential |
uwall_19.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=d_w2ph1 ATthe positions of the wall=+2.4 KAPPAthe force constant for the wall=200
uwall_20The UPPER_WALLS action with label uwall_20 calculates the following quantities: Quantity | Type | Description |
uwall_20.bias | scalar | the instantaneous value of the bias potential |
uwall_20.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=d_w2ph2 ATthe positions of the wall=+2.4 KAPPAthe force constant for the wall=200
uwall_21The UPPER_WALLS action with label uwall_21 calculates the following quantities: Quantity | Type | Description |
uwall_21.bias | scalar | the instantaneous value of the bias potential |
uwall_21.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=d_hgc ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200
uwall_22The UPPER_WALLS action with label uwall_22 calculates the following quantities: Quantity | Type | Description |
uwall_22.bias | scalar | the instantaneous value of the bias potential |
uwall_22.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=d_hgc2 ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200
auwallThe UPPER_WALLS action with label auwall calculates the following quantities: Quantity | Type | Description |
auwall.bias | scalar | the instantaneous value of the bias potential |
auwall.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=a ATthe positions of the wall=+2.6281 KAPPAthe force constant for the wall=400
a1uwallThe UPPER_WALLS action with label a1uwall calculates the following quantities: Quantity | Type | Description |
a1uwall.bias | scalar | the instantaneous value of the bias potential |
a1uwall.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=a1 ATthe positions of the wall=+2.0699 KAPPAthe force constant for the wall=400
a2uwallThe UPPER_WALLS action with label a2uwall calculates the following quantities: Quantity | Type | Description |
a2uwall.bias | scalar | the instantaneous value of the bias potential |
a2uwall.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=a2 ATthe positions of the wall=+1.9018 KAPPAthe force constant for the wall=400
alwallThe LOWER_WALLS action with label alwall calculates the following quantities: Quantity | Type | Description |
alwall.bias | scalar | the instantaneous value of the bias potential |
alwall.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=a ATthe positions of the wall=+2.6281 KAPPAthe force constant for the wall=400
a1lwallThe LOWER_WALLS action with label a1lwall calculates the following quantities: Quantity | Type | Description |
a1lwall.bias | scalar | the instantaneous value of the bias potential |
a1lwall.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=a1 ATthe positions of the wall=+2.0699 KAPPAthe force constant for the wall=400
a2lwallThe LOWER_WALLS action with label a2lwall calculates the following quantities: Quantity | Type | Description |
a2lwall.bias | scalar | the instantaneous value of the bias potential |
a2lwall.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=a2 ATthe positions of the wall=+1.9018 KAPPAthe force constant for the wall=400
uwall_dch1The UPPER_WALLS action with label uwall_dch1 calculates the following quantities: Quantity | Type | Description |
uwall_dch1.bias | scalar | the instantaneous value of the bias potential |
uwall_dch1.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=dch1.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200
uwall_dch2The UPPER_WALLS action with label uwall_dch2 calculates the following quantities: Quantity | Type | Description |
uwall_dch2.bias | scalar | the instantaneous value of the bias potential |
uwall_dch2.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=dch2.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200
uwall_dch3The UPPER_WALLS action with label uwall_dch3 calculates the following quantities: Quantity | Type | Description |
uwall_dch3.bias | scalar | the instantaneous value of the bias potential |
uwall_dch3.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=dch3.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200
uwall_dch4The UPPER_WALLS action with label uwall_dch4 calculates the following quantities: Quantity | Type | Description |
uwall_dch4.bias | scalar | the instantaneous value of the bias potential |
uwall_dch4.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=dch4.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200
uwall_dch5The UPPER_WALLS action with label uwall_dch5 calculates the following quantities: Quantity | Type | Description |
uwall_dch5.bias | scalar | the instantaneous value of the bias potential |
uwall_dch5.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=dch5.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200
uwall_dch6The UPPER_WALLS action with label uwall_dch6 calculates the following quantities: Quantity | Type | Description |
uwall_dch6.bias | scalar | the instantaneous value of the bias potential |
uwall_dch6.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=dch6.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200
uwall_dch7The UPPER_WALLS action with label uwall_dch7 calculates the following quantities: Quantity | Type | Description |
uwall_dch7.bias | scalar | the instantaneous value of the bias potential |
uwall_dch7.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=dch7.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200
uwall_dch8The UPPER_WALLS action with label uwall_dch8 calculates the following quantities: Quantity | Type | Description |
uwall_dch8.bias | scalar | the instantaneous value of the bias potential |
uwall_dch8.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=dch8.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200
uwall_dco1The UPPER_WALLS action with label uwall_dco1 calculates the following quantities: Quantity | Type | Description |
uwall_dco1.bias | scalar | the instantaneous value of the bias potential |
uwall_dco1.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=dco1.mean ATthe positions of the wall=+1.4 KAPPAthe force constant for the wall=200
uwall_dco2The UPPER_WALLS action with label uwall_dco2 calculates the following quantities: Quantity | Type | Description |
uwall_dco2.bias | scalar | the instantaneous value of the bias potential |
uwall_dco2.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=dco2.mean ATthe positions of the wall=+1.4 KAPPAthe force constant for the wall=200
uwall_dco3The UPPER_WALLS action with label uwall_dco3 calculates the following quantities: Quantity | Type | Description |
uwall_dco3.bias | scalar | the instantaneous value of the bias potential |
uwall_dco3.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=dco3.mean ATthe positions of the wall=+1.4 KAPPAthe force constant for the wall=200
uwall_dco4The UPPER_WALLS action with label uwall_dco4 calculates the following quantities: Quantity | Type | Description |
uwall_dco4.bias | scalar | the instantaneous value of the bias potential |
uwall_dco4.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=dco4.mean ATthe positions of the wall=+1.4 KAPPAthe force constant for the wall=200
uwall_dco5The UPPER_WALLS action with label uwall_dco5 calculates the following quantities: Quantity | Type | Description |
uwall_dco5.bias | scalar | the instantaneous value of the bias potential |
uwall_dco5.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=dco5.mean ATthe positions of the wall=+1.4 KAPPAthe force constant for the wall=200
METADUsed to performed metadynamics on one or more collective variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities: Quantity | Type | Description |
metad.bias | scalar | the instantaneous value of the bias potential |
metad.rbias | scalar | the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram. |
metad.rct | scalar | the reweighting factor c(t). |
ARGthe labels of the scalars on which the bias will act=diff
PACEthe frequency for hill addition=100
HEIGHTthe heights of the Gaussian hills=3.0
SIGMAthe widths of the Gaussian hills=0.05
BIASFACTORuse well tempered metadynamics and use this bias factor=50
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=-9.0
GRID_MAXthe upper bounds for the grid=9
GRID_BINthe number of bins for the grid=200
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=diff,d_clo,d_oho,d_ocl,rmsd_cal,rmsd_wat,rmsd_sub,rmsd_all,prod,b_clo,b_oho,b_clm,prod,a,c_h_cl,metad.*
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1