PLUMED-NEST

Project ID: plumID:25.008
Source: chignolin/opes/plumed.dat
Originally used with PLUMED version: 2.10
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. 


#generated with gmx editconf -f topol.tpr -o reference.pdb, see https://www.plumed.org/doc-v2.7/user-doc/html/_m_o_l_i_n_f_o.html
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=chignolin-ref.pdb
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-166

# Select Calpha
PROTEINThe GROUP action with label PROTEIN calculates the following quantities:
 Quantity   
 Type   
 Description  
PROTEIN
atoms
indices of atoms specified in GROUP: 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
CAThe GROUP action with label CA calculates the following quantities:
 Quantity   
 Type   
 Description  
CA
atoms
indices of atoms specified in GROUP: 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=5,26,47,61,73,88,102,109,123,147

rmsd_caThe RMSD action with label rmsd_ca calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd_ca
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=chignolin-ca.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_ca: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=chignolin-ca.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0

d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,5
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,5
d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,26
d4The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
d4
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,5
d5The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Type   
 Description  
d5
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,26
d6The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Type   
 Description  
d6
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,47
d7The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Type   
 Description  
d7
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,5
d8The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Type   
 Description  
d8
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,26
d9The DISTANCE action with label d9 calculates the following quantities:
 Quantity   
 Type   
 Description  
d9
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,47
d10The DISTANCE action with label d10 calculates the following quantities:
 Quantity   
 Type   
 Description  
d10
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=73,61
d11The DISTANCE action with label d11 calculates the following quantities:
 Quantity   
 Type   
 Description  
d11
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,5
d12The DISTANCE action with label d12 calculates the following quantities:
 Quantity   
 Type   
 Description  
d12
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,26
d13The DISTANCE action with label d13 calculates the following quantities:
 Quantity   
 Type   
 Description  
d13
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,47
d14The DISTANCE action with label d14 calculates the following quantities:
 Quantity   
 Type   
 Description  
d14
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,61
d15The DISTANCE action with label d15 calculates the following quantities:
 Quantity   
 Type   
 Description  
d15
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=88,73
d16The DISTANCE action with label d16 calculates the following quantities:
 Quantity   
 Type   
 Description  
d16
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,5
d17The DISTANCE action with label d17 calculates the following quantities:
 Quantity   
 Type   
 Description  
d17
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,26
d18The DISTANCE action with label d18 calculates the following quantities:
 Quantity   
 Type   
 Description  
d18
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,47
d19The DISTANCE action with label d19 calculates the following quantities:
 Quantity   
 Type   
 Description  
d19
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,61
d20The DISTANCE action with label d20 calculates the following quantities:
 Quantity   
 Type   
 Description  
d20
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,73
d21The DISTANCE action with label d21 calculates the following quantities:
 Quantity   
 Type   
 Description  
d21
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=102,88
d22The DISTANCE action with label d22 calculates the following quantities:
 Quantity   
 Type   
 Description  
d22
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,5
d23The DISTANCE action with label d23 calculates the following quantities:
 Quantity   
 Type   
 Description  
d23
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,26
d24The DISTANCE action with label d24 calculates the following quantities:
 Quantity   
 Type   
 Description  
d24
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,47
d25The DISTANCE action with label d25 calculates the following quantities:
 Quantity   
 Type   
 Description  
d25
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,61
d26The DISTANCE action with label d26 calculates the following quantities:
 Quantity   
 Type   
 Description  
d26
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,73
d27The DISTANCE action with label d27 calculates the following quantities:
 Quantity   
 Type   
 Description  
d27
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,88
d28The DISTANCE action with label d28 calculates the following quantities:
 Quantity   
 Type   
 Description  
d28
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=109,102
d29The DISTANCE action with label d29 calculates the following quantities:
 Quantity   
 Type   
 Description  
d29
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,5
d30The DISTANCE action with label d30 calculates the following quantities:
 Quantity   
 Type   
 Description  
d30
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,26
d31The DISTANCE action with label d31 calculates the following quantities:
 Quantity   
 Type   
 Description  
d31
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,47
d32The DISTANCE action with label d32 calculates the following quantities:
 Quantity   
 Type   
 Description  
d32
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,61
d33The DISTANCE action with label d33 calculates the following quantities:
 Quantity   
 Type   
 Description  
d33
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,73
d34The DISTANCE action with label d34 calculates the following quantities:
 Quantity   
 Type   
 Description  
d34
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,88
d35The DISTANCE action with label d35 calculates the following quantities:
 Quantity   
 Type   
 Description  
d35
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,102
d36The DISTANCE action with label d36 calculates the following quantities:
 Quantity   
 Type   
 Description  
d36
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=123,109
d37The DISTANCE action with label d37 calculates the following quantities:
 Quantity   
 Type   
 Description  
d37
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,5
d38The DISTANCE action with label d38 calculates the following quantities:
 Quantity   
 Type   
 Description  
d38
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,26
d39The DISTANCE action with label d39 calculates the following quantities:
 Quantity   
 Type   
 Description  
d39
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,47
d40The DISTANCE action with label d40 calculates the following quantities:
 Quantity   
 Type   
 Description  
d40
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,61
d41The DISTANCE action with label d41 calculates the following quantities:
 Quantity   
 Type   
 Description  
d41
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,73
d42The DISTANCE action with label d42 calculates the following quantities:
 Quantity   
 Type   
 Description  
d42
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,88
d43The DISTANCE action with label d43 calculates the following quantities:
 Quantity   
 Type   
 Description  
d43
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,102
d44The DISTANCE action with label d44 calculates the following quantities:
 Quantity   
 Type   
 Description  
d44
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,109
d45The DISTANCE action with label d45 calculates the following quantities:
 Quantity   
 Type   
 Description  
d45
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=147,123

deepTICAThe PYTORCH_MODEL action with label deepTICA calculates the following quantities:
 Quantity   
 Type   
 Description  
deepTICA.node-0
scalar
Model outputs  This is the 0th of these quantities
deepTICA.node-1
scalar
Model outputs  This is the 1th of these quantities
deepTICA.node-2
scalar
Model outputs  This is the 2th of these quantities
deepTICA.node-3
scalar
Model outputs  This is the 3th of these quantities
deepTICA.node-4
scalar
Model outputs  This is the 4th of these quantities: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=../training/pytorch_files/chignolin_ca_dist_lag1ps_with_koopman.ptc ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45


metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ...
  ARGthe labels of the scalars on which the bias will act=rmsd_ca
  PACEthe frequency for hill addition=500000000
  BIASFACTORuse well tempered metadynamics and use this bias factor=10
  HEIGHTthe heights of the Gaussian hills=0.6
  SIGMAthe widths of the Gaussian hills=0.02
  FILE a file in which the list of added hills is stored=HILLS
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES
...

opesThe OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential
opes.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff
scalar
effective sample size
opes.nker
scalar
total number of compressed kernels used to represent the bias: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
  ARGthe labels of the scalars on which the bias will act=deepTICA.node-0,deepTICA.node-1
  PACEthe frequency for kernel deposition=500
  TEMP temperature=340
  BARRIERthe free energy barrier to be overcome=30
... 
opes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
  ARGthe labels of the scalars on which the bias will act=deepTICA.node-0,deepTICA.node-1
  PACEthe frequency for kernel deposition=500
  TEMP temperature=340
  BARRIERthe free energy barrier to be overcome=30
 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS
... 

# PRINT
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=rmsd_ca,deepTICA.*,opes.*,metad.* FILEthe name of the file on which to output these quantities=COLVAR