PLUMED-NEST

Project ID: plumID:19.060
Source: 1_wolfe_quapp_potential/single_replica/inputs/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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units

The UNITS action with label  calculates something
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=../../../0_code/NeuralNetworkVes.cpp

p: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=1
The POSITION action with label p calculates the following quantities:
 Quantity   
 Description  
p.x
the x-component of the atom position
p.y
the y-component of the atom position
p.z
the z-component of the atom positionene: 
ENERGY
Calculate the total potential energy of the simulation box. More details

# nn bias
The ENERGY action with label ene calculates something
NN_VES
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
LABEL=nn
ARG=p.x
NODES=48,24,12 
OPTIM=ADAM
ACTIVATION=RELU
GRID_MIN=-3 
GRID_MAX=3
GRID_BIN=50 
TEMP=1
AVE_STRIDE=500 
PRINT_STRIDE=1000 
TARGET_STRIDE=1
GAMMA=10
LRATE=0.001
TAU_KL=50000
DECAY=5000
ADAPTIVE_DECAY=0.5
... NN_VES

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
ARG
the labels of the values that you would like to print to the file
 
FILE
the name of the file on which to output these quantities
=COLVAR 
FMT
the format that should be used to output real numbers
=%10.8f