PLUMED-NEST

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

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=coordination_multi.cpp
The LOAD action with label  calculates somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=MemFusionP_NP.cpp
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=pytorch_model_bias.cpp

NP: 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 NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=NP
The GROUP action with label NP calculates somethingtails: 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 NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=tails
The GROUP action with label tails calculates somethinginnerheads: 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 NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=innerheads
The GROUP action with label innerheads calculates somethingmus4: 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 NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=MUS4

The GROUP action with label mus4 calculates somethingcom: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=NP

# Chain coordinate value

The CENTER action with label com calculates the following quantities:
 Quantity   
 Description  
com.value
the position of the center of massmemFusion: MEMFUSIONP_NPThis action is not part of PLUMED and was included by using a LOAD command More details NP=com TAILS=tails NSMEM=20 DSMEM=0.1 ZSHIFT=1.1 RCYLMEM=2.0

# Ligand coordination numbers

c_mus4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=mus4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=innerheads R_0The r_0 parameter of the switching function=0.8 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.1 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=1

# Lipid tail coordination numbers in concentrical spherical shells

The COORDINATION action with label c_mus4 calculates the following quantities:
 Quantity   
 Description  
c_mus4.value
the value of the coordinationc_tails: COORDINATION_MULTIThis action is not part of PLUMED and was included by using a LOAD command More details GROUPA=com GROUPB=tails D_0=0.0 R_0=1.6,1.7,1.8,1.9,2.0,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,3.0,3.1,3.2,3.3 NN=50 MM=100 D_MAX=3.6 NLIST NL_CUTOFF=3.8 NL_STRIDE=10 N_OUT=18 Z_SHIFT=1 XY_RADIUS=2

c_0: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.0,c_tails.1 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_0 calculates the following quantities:
 Quantity   
 Description  
c_0.value
an arbitrary functionc_1: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.1,c_tails.2 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_1 calculates the following quantities:
 Quantity   
 Description  
c_1.value
an arbitrary functionc_2: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.2,c_tails.3 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_2 calculates the following quantities:
 Quantity   
 Description  
c_2.value
an arbitrary functionc_3: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.3,c_tails.4 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_3 calculates the following quantities:
 Quantity   
 Description  
c_3.value
an arbitrary functionc_4: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.4,c_tails.5 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_4 calculates the following quantities:
 Quantity   
 Description  
c_4.value
an arbitrary functionc_5: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.5,c_tails.6 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_5 calculates the following quantities:
 Quantity   
 Description  
c_5.value
an arbitrary functionc_6: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.6,c_tails.7 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_6 calculates the following quantities:
 Quantity   
 Description  
c_6.value
an arbitrary functionc_7: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.7,c_tails.8 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_7 calculates the following quantities:
 Quantity   
 Description  
c_7.value
an arbitrary functionc_8: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.8,c_tails.9 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_8 calculates the following quantities:
 Quantity   
 Description  
c_8.value
an arbitrary functionc_9: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.9,c_tails.10 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_9 calculates the following quantities:
 Quantity   
 Description  
c_9.value
an arbitrary functionc_10: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.10,c_tails.11 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_10 calculates the following quantities:
 Quantity   
 Description  
c_10.value
an arbitrary functionc_11: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.11,c_tails.12 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_11 calculates the following quantities:
 Quantity   
 Description  
c_11.value
an arbitrary functionc_12: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.12,c_tails.13 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_12 calculates the following quantities:
 Quantity   
 Description  
c_12.value
an arbitrary functionc_13: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.13,c_tails.14 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_13 calculates the following quantities:
 Quantity   
 Description  
c_13.value
an arbitrary functionc_14: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.14,c_tails.15 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_14 calculates the following quantities:
 Quantity   
 Description  
c_14.value
an arbitrary functionc_15: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.15,c_tails.16 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c_15 calculates the following quantities:
 Quantity   
 Description  
c_15.value
an arbitrary functionc_16: CUSTOMCalculate a combination of variables using a custom expression. More details VARthe names to give each of the arguments in the function=x,y ARGthe values input to this function=c_tails.16,c_tails.17 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO


# Lower wall on ligan coordination number

The CUSTOM action with label c_16 calculates the following quantities:
 Quantity   
 Description  
c_16.value
an arbitrary functionlwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=c_mus4 ATthe positions of the wall=70 KAPPAthe force constant for the wall=1000

# Committor bias

The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialPYTORCH_MODEL_BIASThis action is not part of PLUMED and was included by using a LOAD command More details ...
    LABEL=model
    FILE=model_0_z.pt 
    ARG=c_0,c_1,c_2,c_3,c_4,c_5,c_6,c_7,c_8,c_9,c_10,c_11,c_12,c_13,c_14,c_15,c_16 
    LAMBDA=20
    BETA=0.4
    EPSILON=1
    SIGMOID_P=3
    USE_Q_FOR_BIAS
...

potential: 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=model.kbias

# Opes bias

The BIASVALUE action with label potential calculates the following quantities:
 Quantity   
 Description  
potential.bias
the instantaneous value of the bias potential
potential._bias
one or multiple instances of this quantity can be referenced elsewhere in the input fileOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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=model.z
	PACEthe frequency for kernel deposition=500 
	SIGMA the initial widths of the kernels, divided by the square root of gamma=0.02
	BARRIERthe free energy barrier to be overcome=30 
	TEMP temperature=310 
        #STATE_RFILE=State.data
        STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=State.data
	STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=500*100
...

The OPES_METAD_EXPLORE action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the biasPRINTPrint quantities to a file. More details 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 ARGthe labels of the values that you would like to print to the file=*