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=../../plumed_so/OPESmetad.so
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../../plumed_so/WalkerAggregator.so
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../../plumed_so/pytorch_model_bias.so
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../../plumed_so/MM_Energy.so


dASPGLY: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=45,106
The DISTANCE action with label dASPGLY calculates the following quantities:
 Quantity   
 Description  
dASPGLY.value
the DISTANCE between this pair of atomsdASPTHR: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=45,120

# Approximate protein energy
The DISTANCE action with label dASPTHR calculates the following quantities:
 Quantity   
 Description  
dASPTHR.value
the DISTANCE between this pair of 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=1-166

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=1,5,7,10,11,13,15,16,18,20,22,23,24,26,28,31,32,34,36,37,39,41,43,44,45,47,49,52,53,54,55,56,57,58,61,63,66,69,70,71,73,75,78,81,82,83,84,85,86,88,90,92,94,98,99,100,102,105,106,107,109,111,113,115,119,120,121,123,125,128,129,131,133,134,135,137,139,141,143,144,145,147,149,152,153,155,157,158,160,162,164,165,166

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=80 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=../../../models/model_0_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=16 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-1.9065
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=20 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,dASPGLY,dASPTHR,z.node-0,bias,opes.*  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