PLUMED-NEST

Project ID: plumID:25.012
Source: OPES_Enhanced_Sampling_with_Committor/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

#! vim:ft=plumed
#RESTART
# input file for unbiased amylase reaction 

#UNITS
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A

# load interface for bias computation
The UNITS action with label  calculates somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=./pytorch_model_bias.so

ene: ENERGYCalculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingcell: CELLGet the components of the simulation cell More details

# ==== DISTANCES =====
The CELL action with label cell calculates the following quantities:
 Quantity   
 Description  
cell.ax
the ax component of the cell matrix
cell.ay
the ay component of the cell matrix
cell.az
the az component of the cell matrix
cell.bx
the bx component of the cell matrix
cell.by
the by component of the cell matrix
cell.bz
the bz component of the cell matrix
cell.cx
the cx component of the cell matrix
cell.cy
the cy component of the cell matrix
cell.cz
the cz component of the cell matrixINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details FILEfile to be included=plumed_distances_49descriptors.dat

# ==== POSITIONS =====
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details FILEfile to be included=plumed_positions_49descriptors.dat


# ==== CVs for 2D FES =====
CN_Ogly_acid_proton: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=7699 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=26289 R_0The r_0 parameter of the switching function=2.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=3.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100
The COORDINATION action with label CN_Ogly_acid_proton calculates the following quantities:
 Quantity   
 Description  
CN_Ogly_acid_proton.value
the value of the coordinationCN_SugO2_acid_proton: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=7704 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=26289 R_0The r_0 parameter of the switching function=2.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=3.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100
The COORDINATION action with label CN_SugO2_acid_proton calculates the following quantities:
 Quantity   
 Description  
CN_SugO2_acid_proton.value
the value of the coordinationCN_Ogly_water_proton: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=7699 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3607,26288 R_0The r_0 parameter of the switching function=2.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=3.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100
The COORDINATION action with label CN_Ogly_water_proton calculates the following quantities:
 Quantity   
 Description  
CN_Ogly_water_proton.value
the value of the coordinationCN_water_acid_proton: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26287 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=26289 R_0The r_0 parameter of the switching function=2.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=3.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100
The COORDINATION action with label CN_water_acid_proton calculates the following quantities:
 Quantity   
 Description  
CN_water_acid_proton.value
the value of the coordinationCN_acid_water_proton: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3606 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3607,26288 R_0The r_0 parameter of the switching function=2.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=3.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100

The COORDINATION action with label CN_acid_water_proton calculates the following quantities:
 Quantity   
 Description  
CN_acid_water_proton.value
the value of the coordinationCV_SN2: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=D_subst_C1-subst_Ogly,D_Asp197_O1-subst_C1 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
The COMBINE action with label CV_SN2 calculates the following quantities:
 Quantity   
 Description  
CV_SN2.value
a linear compbinationCV_PT: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=CN_Ogly_acid_proton,CN_SugO2_acid_proton,CN_Ogly_water_proton COEFFICIENTS the coefficients of the arguments in your function=-1,-1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The COMBINE action with label CV_PT calculates the following quantities:
 Quantity   
 Description  
CV_PT.value
a linear compbinationCV_acid-water: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=CN_water_acid_proton,CN_acid_water_proton 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


# ==== WALL =====
#UPPER_WALLS ARG=D_C_subst_C1-Water_O AT=+3.5 KAPPA=1000.0 EXP=2 LABEL=uwall_D_C_subst_C1-Water_O


# ==== COMPUTE COMMITTOR GUESS FOR BIAS ====

The COMBINE action with label CV_acid-water calculates the following quantities:
 Quantity   
 Description  
CV_acid-water.value
a linear compbinationz: PYTORCH_MODEL_BIASThis action is not part of PLUMED and was included by using a LOAD command More details FILE=model_test3_cycle2_zeta.pt ARG=D_Asp197_CA-subst_O5,D_Asp197_CA-subst_C1,D_Asp197_CA-subst_C2,D_Asp197_CA-subst_C3,D_Asp197_CA-subst_C4,D_Asp197_CA-subst_C5,D_Asp197_CA-subst_O6,D_Asp197_C-Asp197_O1,D_Asp197_C-Asp197_O2,D_Asp197_O1-subst_O5,D_Asp197_O1-subst_C1,D_Asp197_O1-subst_C2,D_Asp197_O1-subst_O6H,D_Asp197_O2-subst_O5,D_Asp197_O2-subst_C1,D_Asp197_O2-subst_C2,D_Asp197_O2-subst_O6H,D_subst_C1-subst_O5,D_subst_O5-O5dash,D_subst_C1-subst_C1H,D_subst_C1-subst_C2,D_subst_C1-subst_Ogly,D_subst_C1-C1dash,D_subst_C2-C2dash,D_Asp300_O1-subst_O2H,D_Asp300_O2-subst_O2H,D_subst_C3-C3dash,D_Asp300_O1-subst_O3H,D_Asp300_O2-subst_O3H,D_subst_C4-C4dash,D_subst_C5-C5dash,D_subst_O6-O6dash,D_subst_Ogly-subst_C4dash,D_subst_Ogly-Glu233_H,D_subst_Ogly-Water_O,D_subst_O6dash-Water_O,D_Glu233_C-Glu233_O1,D_Glu233_C-Glu233_O2,D_Glu233_O1-Glu233_H,D_Glu233_O1-subst_O3Hdash,D_Glu233_O2-Glu233_H,D_Glu233_O2-Water_O,D_Glu233_O2-subst_O3Hdash,D_subst_O2-Glu233_H,D_Asp300_O1-Water_O,D_Asp300_O2-Water_O,D_subst_O2-Water_O,sin_D_torsion1,cos_D_torsion1,sin_D_torsion2,cos_D_torsion2 LAMBDA=1.0 EPSILON=1e-7

q: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=z.node-0 varthe names to give each of the arguments in the function=z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=1/(1+exp(-3*z))
 
# this is the total bias
The CUSTOM action with label q calculates the following quantities:
 Quantity   
 Description  
q.value
an arbitrary functionbias: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=z.bias-0,q varthe names to give each of the arguments in the function=zbias,q PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=-2.5*(zbias+2*log(q+0.00000000001)+2*log(1.00000000001-q))
#### Range of lambda could be from 0.6*kBT=1.5 to 1.0*kBT=2.5 ####

#bias: CUSTOM ARG=z.bias-0,q var=zbias,q PERIODIC=NO FUNC=-2.5*(zbias+2*log(q+0.00000000001)+2*log(1.00000000001-q)+30)  #### Here, lambda=kBT=2.5 ####
#bias: CUSTOM ARG=z.bias-0,q var=zbias,q PERIODIC=NO FUNC=-lambda*(zbias+2*log(q+0.00000000001)+2*log(1.00000000001-q)+30)   ###### Change the lambda value here while using zeta bias with single lambda.########### "30" is added to make the bias centered around zero. ###########

The CUSTOM action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
an arbitrary functionpotential: 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=bias     ########### Use this line while using zeta bias with single lambda, and comment out next two lines. #############
# Once the committor model is converged, ideally zeta bias is not required, only opes bias should be enough for the transition between
# the metastable basins. Still zeta bias can be used, and while reweighting, we need to add up zeta bias and opes bias.

#ecv: ECV_LINEAR ARG=bias TEMP=300 LAMBDA_MIN=0.0 LAMBDA_MAX=2 LAMBDA_STEPS=25
#opes: OPES_EXPANDED ARG=ecv.* PACE=300 #RESTART=YES

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: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. More details ...
    ARGthe labels of the scalars on which the bias will act=z.node-0
    BARRIERthe free energy barrier to be overcome=80  #activation barrier of step1 = 13.9 kcal/mol = 58.16 kJ/mol; from intermediate it is 19 kcal/mol.
#    BARRIER=65  #activation barrier of step2 = 16 kcal/mol = 66.94 kJ/mol
#    SIGMA=0.1
    PACEthe frequency for kernel deposition=100
    TEMP temperature=300.0
    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=State.data 
#    STATE_RFILE=Restart.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=100 
    #RESTART=YES
#    COMPRESSION_THRESHOLD=0.5
#    EXTRA_BIAS=potential.bias_bias
# Once the protocol is fixed with one replica, try to use multiple walkers if it is possible with CP2K.
# It will help to reach the static bias faster.
...

# ==== PRINT STUFF ====
The OPES_METAD 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 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=* STRIDE the frequency with which the quantities of interest should be output=1
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR_plot ARGthe labels of the values that you would like to print to the file=CV_SN2,CV_PT,CV_acid-water,D_Asp197_O1-subst_C1,D_subst_C1-subst_Ogly,potential.bias_bias,q,z.node-0,opes.bias STRIDE the frequency with which the quantities of interest should be output=1

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=C_Asp197_CA.*,C_Asp197_C.*,C_Asp197_O1.*,C_Asp197_O2.*,C_subst_O5.*,C_subst_C1.*,C_subst_C1H.*,C_subst_C2.*,C_subst_O2H.*,C_subst_C3.*,C_subst_O3H.*,C_subst_C4.*,C_subst_C5.*,C_subst_O6.*,C_subst_O6H.*,C_subst_Ogly.*,C_subst_O5dash.*,C_subst_C1dash.*,C_subst_C2dash.*,C_subst_C3dash.*,C_subst_C4dash.*,C_subst_C5dash.*,C_subst_O6dash.*,C_Glu233_C.*,C_Glu233_O1.*,C_Glu233_O2.*,C_Glu233_H.*,C_Asp300_O1.*,C_Asp300_O2.*,C_Water_O.*,C_subst_O2.*,C_subst_O3Hdash.*,potential.bias_bias,opes.bias,q,z.node-0 STRIDE the frequency with which the quantities of interest should be output=20 FILEthe name of the file on which to output these quantities=COLVAR_position_bias

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