PLUMED-NEST

Project ID: plumID:26.002
Source: MUOR_APO_old_RMSD_PATH/0/plumed.dat
Originally used with PLUMED version: 2.9.1
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

#SETTINGS NATOMS=2000000
#RESTART

p1: PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=../final_path.pdb LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=200.0
The PATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.sss
the position on the path
p1.zzz
the distance from the pathuwallZ: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.zzz ATthe positions of the wall=0.15 KAPPAthe force constant for the wall=2500.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0
The UPPER_WALLS action with label uwallZ calculates the following quantities:
 Quantity   
 Description  
uwallZ.bias
the instantaneous value of the bias potential
uwallZ.force2
the instantaneous value of the squared force due to this bias potentiallwallS: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.sss ATthe positions of the wall=1.3 KAPPAthe force constant for the wall=5000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0
The LOWER_WALLS action with label lwallS calculates the following quantities:
 Quantity   
 Description  
lwallS.bias
the instantaneous value of the bias potential
lwallS.force2
the instantaneous value of the squared force due to this bias potentialszparab: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p1.sss,p1.zzz FUNCthe function you wish to evaluate=y+(0.00085*(x-8.5)^2)-0.07 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label szparab calculates the following quantities:
 Quantity   
 Description  
szparab.value
an arbitrary functionuwallsz: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=szparab ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=200000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0

The UPPER_WALLS action with label uwallsz calculates the following quantities:
 Quantity   
 Description  
uwallsz.bias
the instantaneous value of the bias potential
uwallsz.force2
the instantaneous value of the squared force due to this bias potentialr3: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../8k9k_soloCA_fix2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
The RMSD action with label r3 calculates the following quantities:
 Quantity   
 Description  
r3.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputr4: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../inactive_state.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL 

The RMSD action with label r4 calculates the following quantities:
 Quantity   
 Description  
r4.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputSC157: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1455,1457,1461,1464
The CENTER action with label SC157 calculates the following quantities:
 Quantity   
 Description  
SC157.value
the position of the center of massSC246: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=2907,2910,2913
The CENTER action with label SC246 calculates the following quantities:
 Quantity   
 Description  
SC246.value
the position of the center of massSC291: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=3680,3683,3684,3686,3688,3690,3692
The CENTER action with label SC291 calculates the following quantities:
 Quantity   
 Description  
SC291.value
the position of the center of massd157-246: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC157,SC246
The DISTANCE action with label d157-246 calculates the following quantities:
 Quantity   
 Description  
d157-246.value
the DISTANCE between this pair of atomsd157-291: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC157,SC291
The DISTANCE action with label d157-291 calculates the following quantities:
 Quantity   
 Description  
d157-291.value
the DISTANCE between this pair of atomsd246-291: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC246,SC291
The DISTANCE action with label d246-291 calculates the following quantities:
 Quantity   
 Description  
d246-291.value
the DISTANCE between this pair of atomsPIF1-path: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p1.sss,d157-246 FUNCthe function you wish to evaluate=y+(0.003*(x^2))-1.22 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label PIF1-path calculates the following quantities:
 Quantity   
 Description  
PIF1-path.value
an arbitrary functionPIF2-path: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p1.sss,d157-291 FUNCthe function you wish to evaluate=y+(0.003*(x^2))-1.22 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label PIF2-path calculates the following quantities:
 Quantity   
 Description  
PIF2-path.value
an arbitrary functionPIF3-path: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p1.sss,d246-291 FUNCthe function you wish to evaluate=y+(0.003*(x^2))-1.45 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label PIF3-path calculates the following quantities:
 Quantity   
 Description  
PIF3-path.value
an arbitrary functionuwallPIF: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=PIF1-path,PIF2-path,PIF3-path ATthe positions of the wall=0.0,0.0,0.0 KAPPAthe force constant for the wall=5000.0,5000.0,5000.0 EXP the powers for the walls=2,2,2 EPS the values for s_i in the expression for a wall=1,1,1 OFFSET the offset for the start of the wall=0,0,0

#sidechain of Y5.58
The UPPER_WALLS action with label uwallPIF calculates the following quantities:
 Quantity   
 Description  
uwallPIF.bias
the instantaneous value of the bias potential
uwallPIF.force2
the instantaneous value of the squared force due to this bias potentialSC254: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=3038,3041,3042,3044,3046,3047,3049,3051
#sidechain of Y7.53
The CENTER action with label SC254 calculates the following quantities:
 Quantity   
 Description  
SC254.value
the position of the center of massSC338: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=4443,4446,4447,4449,4451,4452,4454,4456
#sidechain of N7.49
The CENTER action with label SC338 calculates the following quantities:
 Quantity   
 Description  
SC338.value
the position of the center of massSC334: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=4380,4383,4384,4385
#sidechain of D2.50
The CENTER action with label SC334 calculates the following quantities:
 Quantity   
 Description  
SC334.value
the position of the center of massSC116: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=813,816,817,818
The CENTER action with label SC116 calculates the following quantities:
 Quantity   
 Description  
SC116.value
the position of the center of massd254-338: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC254,SC338
The DISTANCE action with label d254-338 calculates the following quantities:
 Quantity   
 Description  
d254-338.value
the DISTANCE between this pair of atomsd254-334: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC254,SC334
The DISTANCE action with label d254-334 calculates the following quantities:
 Quantity   
 Description  
d254-334.value
the DISTANCE between this pair of atomsd334-116: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC334,SC116
The DISTANCE action with label d334-116 calculates the following quantities:
 Quantity   
 Description  
d334-116.value
the DISTANCE between this pair of atomsd254-338-path: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p1.sss,d254-338 FUNCthe function you wish to evaluate=y+(0.003*(x^2))-1.6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label d254-338-path calculates the following quantities:
 Quantity   
 Description  
d254-338-path.value
an arbitrary functionuwallNPxxY: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d254-338-path ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=5000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0

The UPPER_WALLS action with label uwallNPxxY calculates the following quantities:
 Quantity   
 Description  
uwallNPxxY.bias
the instantaneous value of the bias potential
uwallNPxxY.force2
the instantaneous value of the squared force due to this bias potentialWO: 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=43897-119656:4    #water oxygen atoms
The GROUP action with label WO calculates somethingyycenter1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=4452,3622,1511 #Leu160 Cgamma, Val287 Cbeta, Tyr338 OH
The CENTER action with label yycenter1 calculates the following quantities:
 Quantity   
 Description  
yycenter1.value
the position of the center of massyywo: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=yycenter1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.30 NN=2 MM=6 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=50
The COORDINATION action with label yywo calculates the following quantities:
 Quantity   
 Description  
yywo.value
the value of the coordinationcon254: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC254 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC338 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.90 NN=8 MM=12}
The COORDINATION action with label con254 calculates the following quantities:
 Quantity   
 Description  
con254.value
the value of the coordinationyywoprod: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=yywo,con254 FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label yywoprod calculates the following quantities:
 Quantity   
 Description  
yywoprod.value
an arbitrary functionyywosum: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=yywo,con254 FUNCthe function you wish to evaluate=x+y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

#sidechain of T105-2.39
The CUSTOM action with label yywosum calculates the following quantities:
 Quantity   
 Description  
yywosum.value
an arbitrary functionSC105: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=634,636,640
#sidechain of R167-3.50
The CENTER action with label SC105 calculates the following quantities:
 Quantity   
 Description  
SC105.value
the position of the center of massSC167: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1608,1611,1614,1617,1619,1620,1623
#sidechain of T281-6.34
The CENTER action with label SC167 calculates the following quantities:
 Quantity   
 Description  
SC167.value
the position of the center of massSC281: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=3516,3518,3522
#sidechain of V171-3.54
The CENTER action with label SC281 calculates the following quantities:
 Quantity   
 Description  
SC281.value
the position of the center of massSC171: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1682,1684,1688
#sidechain of L277-6.30
The CENTER action with label SC171 calculates the following quantities:
 Quantity   
 Description  
SC171.value
the position of the center of massSC277: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=3430,3433,3435,3439
The CENTER action with label SC277 calculates the following quantities:
 Quantity   
 Description  
SC277.value
the position of the center of massd167-105: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC167,SC105
The DISTANCE action with label d167-105 calculates the following quantities:
 Quantity   
 Description  
d167-105.value
the DISTANCE between this pair of atomsd167-281: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC167,SC281
The DISTANCE action with label d167-281 calculates the following quantities:
 Quantity   
 Description  
d167-281.value
the DISTANCE between this pair of atomsd171-277: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC171,SC277

The DISTANCE action with label d171-277 calculates the following quantities:
 Quantity   
 Description  
d171-277.value
the DISTANCE between this pair of atomsene: ENERGYCalculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingvol: VOLUMECalculate the volume the simulation box. More details
The VOLUME action with label vol calculates the volume of simulation boxintene: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=ene,vol FUNCthe function you wish to evaluate=x+0.06022140857*y

The CUSTOM action with label intene calculates the following quantities:
 Quantity   
 Description  
intene.value
an arbitrary functionOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes
  ARGthe labels of the scalars on which the bias will act=p1.sss
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.05
  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=compressed1.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed1.Kernels
  PACEthe frequency for kernel deposition=50000
  BARRIERthe free energy barrier to be overcome=100
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
... OPES_METAD_EXPLORE

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=* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500