PLUMED-NEST-TEST-SITE

Project ID: plumID:19.060
Source: 3_ala4/simulation/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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../../0_code/NeuralNetworkVes.cpp

The LOAD action with label  calculates somethingphi1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15
The TORSION action with label phi1 calculates the following quantities:
 Quantity   
 Description  
phi1.value
the TORSION involving these atomsphi2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,17,19,25
The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Description  
phi2.value
the TORSION involving these atomsphi3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=25,27,29,35
The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Description  
phi3.value
the TORSION involving these atomspsi1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17
The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Description  
psi1.value
the TORSION involving these atomspsi2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=17,19,25,27
The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Description  
psi2.value
the TORSION involving these atomspsi3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=27,29,35,37

# the following is a fake example using the grid-based version
# see below ENDPLUMED for the MC-based version used in the paper

The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Description  
psi3.value
the TORSION involving these atomsNN_VESThis action is not part of PLUMED and was included by using a LOAD command More details ...
  TEMP=300.0
  LABEL=bias
  ARG=phi1,phi2,phi3,psi1,psi2,psi3
  NODES=96,48,24
  OPTIM=ADAM
  ACTIVATION=RELU
  GRID_MIN=-pi,-pi,-pi,-pi,-pi,-pi
  GRID_MAX=pi,pi,pi,pi,pi,pi
  GRID_BIN=10,10,10,10,10,10 # set to 10 to avoid std_bad_alloc
  AVE_STRIDE=500
  PRINT_STRIDE=100
  TARGET_STRIDE=1
  LRATE=0.001
  GAMMA=10
  TAU_KL=100000
  DECAY=2000
  ADAPTIVE_DECAY=20
... NN_VES


PRINTPrint quantities to a file. More details 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=100 FILEthe name of the file on which to output these quantities=COLVAR

ENDPLUMEDTerminate plumed input. More details

# The following input is related to the MC-based version used in the paper. 
This is not compatible with newer plumed versions, if you want to try it you should use the code NeuralNetworkVes_ORIGINAL.cpp. 

NN_VES ...
  TEMP=300.0
  LABEL=bias
  ARG=phi1,phi2,phi3,psi1,psi2,psi3
  NODES=96,48,24
  OPTIM=ADAM
  ACTIVATION=RELU
  GRID_MIN=-pi,-pi,-pi,-pi,-pi,-pi
  GRID_MAX=pi,pi,pi,pi,pi,pi
  GRID_BIN=300,300,300,300,300,300
  AVE_STRIDE=500
  PRINT_STRIDE=100
  TARGET_STRIDE=1
  LRATE=0.001
  GAMMA=10
  TAU_KL=100000
  MODE_DECAY=4
  DECAY_STEP_START=10000
  DECAY=2000
  ADAPTIVE_DECAY=20
  MC_POINTS=20000
  MC_SIGMA=0.5,0.5,0.5,0.5,0.5,0.5
  CALC_MC_ERR=0
  MC_CONVERGENCE_TEST=0
  L2_weight=0.2
  SERIAL
  CALC_RCT
... NN_VES