PLUMED-NEST

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. 
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=nm TIMEthe units of time=ps ENERGYthe units of energy=kj/mol

The UNITS action with label  calculates somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=OPESmetad.so
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=WalkerAggregator.so
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=pytorch_model_bias.so
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=MM_Energy.so

phi: 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 phi calculates the following quantities:
 Quantity   
 Description  
phi.value
the TORSION involving these atomspsi: 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 psi calculates the following quantities:
 Quantity   
 Description  
psi.value
the TORSION involving these atomstheta: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=6,5,7,9

# Approximate protein energy
The TORSION action with label theta calculates the following quantities:
 Quantity   
 Description  
theta.value
the TORSION involving these atomsprot: 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=1-22
The GROUP action with label prot calculates somethingheavy: 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=2,5,6,7,9,11,15,16,17,19
The GROUP action with label heavy calculates somethingE: MM_ENERGYThis action is not part of PLUMED and was included by using a LOAD command More details GROUP=prot FORCE_ATOMS=heavy BONDS_FILE=../bonds_mm.dat ANGLES_FILE=../angles_mm.dat DIHEDRALS_FILE=../dihedrals_mm.dat NONBONDED_LJ LJ_CUTOFF=1.2 LJ_PERATOM_FILE=../lj_peratom_mm.dat LJ_COMB=LB NONBONDED_COULOMB CHARGES_FILE=../charges_mm.dat EPSILON_R=1 EXCLUDE_12 EXCLUDE_13 SCALE_14=0

agg: WALKER_AGGREGATORThis action is not part of PLUMED and was included by using a LOAD command More details ARG=E METHOD=COLLECT WAIT_ALL WALKERS_N=20 WALKERS_MPI WALKERS_ID=@replicas:This keyword specifies that different replicas have different values for this quantity.  See here for more details.{0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19}

z: PYTORCH_MODEL_BIASThis action is not part of PLUMED and was included by using a LOAD command More details FILE=../../../../modelslr/model_2_trivial.pt  ARG=agg.w0,agg.w1,agg.w2,agg.w3,agg.w4,agg.w5,agg.w6,agg.w7,agg.w8,agg.w9,agg.w10,agg.w11,agg.w12,agg.w13,agg.w14,agg.w15,agg.w16,agg.w17,agg.w18,agg.w19 LAMBDA=8.02 EPSILON=1e-7

bias: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=z.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-0.0033
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

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_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ARGthe labels of the scalars on which the bias will act=z.node-0 PACEthe frequency for kernel deposition=500 BARRIERthe free energy barrier to be overcome=40 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=compressed.Kernels STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels WALKERS_MPI switch on MPI version of multiple walkers AGGREGATED 

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 ARGthe labels of the values that you would like to print to the file=E,phi,psi,theta,z.node-0,bias  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