PLUMED-NEST

Project ID: plumID:24.011
Source: dasa/data/template/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

# input file for unbiased dasa 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.cpp
#LOAD FILE=./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

# ==== GROUPS ====
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 matrixC: 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=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15
The GROUP action with label C calculates somethingN: 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=16
The GROUP action with label N calculates somethingO: 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=17,18,19,20,21
The GROUP action with label O calculates somethingH: 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=22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42

# ==== DISTANCES =====
The GROUP action with label H calculates somethingINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details FILEfile to be included=./plumed_distances.dat

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

# ==== COMPUTE COMMITTOR BIAS ====
q: PYTORCH_MODEL_BIASThis action is not part of PLUMED and was included by using a LOAD command More details FILE=../../models/model.pt ARG=x1,x2,x3,x4,x5,x6,x7,x8,x9,x10,x11,x12,x13,x14,x15,x16,x17,x18,x19,x20,x21,x22,x23,x24,x25,x26,x27,x28,x29,x30,x31,x32,x33,x34,x35,x36,x37,x38,x39,x40,x41,x42,x43,x44,x45 LAMBDA=3 EPSILON=1e-7

# this is the total bias
bias: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q.bias-0 varthe names to give each of the arguments in the function=a PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=-a

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


# ==== PRINT STUFF ====
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 filePRINTPrint 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=20