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

# Approximate protein energy
prot: 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=1-272

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=1,5,7,10,11,12,13,14,15,17,19,23,24,25,27,29,32,33,35,37,38,40,42,44,45,46,48,50,54,55,56,58,60,63,66,67,68,71,72,73,75,77,80,81,83,85,86,87,89,91,93,95,96,97,99,101,104,106,110,114,115,116,118,120,124,125,126,128,130,133,134,135,136,137,138,140,143,144,145,147,150,151,152,153,156,158,161,164,165,166,168,170,173,175,176,177,179,181,184,186,187,188,190,193,194,195,197,199,202,205,208,210,211,214,217,218,219,220,223,225,228,231,232,233,234,237,239,242,245,246,247,248,251,253,256,259,260,261,263,265,268,270,271,272

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 NLIST NL_STRIDE=10 NL_SKIN=0.24

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=30 EPSILON=1e-7 BIAS_STRIDE=1

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-0.0020
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 STRIDEthe frequency with which the forces due to the bias should be calculated=1

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=1000 BARRIERthe free energy barrier to be overcome=40 FILE a file in which the list of all deposited kernels is stored=../0/Kernels.data STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=../0/compressed.Kernels STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=../0/compressed.Kernels WALKERS_MPI switch on MPI version of multiple walkers AGGREGATED STRIDEthe frequency with which the forces due to the bias should be calculated=1

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,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