PLUMED-NEST

Project ID: plumID:25.020
Source: apoADRB1/0/plumed.dat
Originally used with PLUMED version: 2.9
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=90.71
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+(0.00111*(x-7)^2)-0.05 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=7bts_soloCA_fix.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

#PIF
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 inputSC94: 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=1438,1440,1444,1447
The CENTER action with label SC94 calculates the following quantities:
 Quantity   
 Description  
SC94.value
the position of the center of massSC184: 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=2885,2888,2891
The CENTER action with label SC184 calculates the following quantities:
 Quantity   
 Description  
SC184.value
the position of the center of massSC227: 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=3613,3616,3617,3619,3621,3623,3625
The CENTER action with label SC227 calculates the following quantities:
 Quantity   
 Description  
SC227.value
the position of the center of massd94-184: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC94,SC184
The DISTANCE action with label d94-184 calculates the following quantities:
 Quantity   
 Description  
d94-184.value
the DISTANCE between this pair of atomsd94-227: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC94,SC227
The DISTANCE action with label d94-227 calculates the following quantities:
 Quantity   
 Description  
d94-227.value
the DISTANCE between this pair of atomsd184-227: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC184,SC227
The DISTANCE action with label d184-227 calculates the following quantities:
 Quantity   
 Description  
d184-227.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,d94-184 FUNCthe function you wish to evaluate=y+(0.0045*(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,d94-227 FUNCthe function you wish to evaluate=y+(0.0045*(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,d184-227 FUNCthe function you wish to evaluate=y+(0.0045*(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

#NPxxY
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 potentialSC192: 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=3014,3017,3018,3020,3022,3023,3025,3027
The CENTER action with label SC192 calculates the following quantities:
 Quantity   
 Description  
SC192.value
the position of the center of massSC271: 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=4353,4356,4357,4359,4361,4362,4364,4366
The CENTER action with label SC271 calculates the following quantities:
 Quantity   
 Description  
SC271.value
the position of the center of massSC267: 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=4287,4290,4291,4292
The CENTER action with label SC267 calculates the following quantities:
 Quantity   
 Description  
SC267.value
the position of the center of massSC52: 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=418,419,420,421
The CENTER action with label SC52 calculates the following quantities:
 Quantity   
 Description  
SC52.value
the position of the center of massd192-271: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC192,SC271
The DISTANCE action with label d192-271 calculates the following quantities:
 Quantity   
 Description  
d192-271.value
the DISTANCE between this pair of atomsd192-267: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC192,SC267
The DISTANCE action with label d192-267 calculates the following quantities:
 Quantity   
 Description  
d192-267.value
the DISTANCE between this pair of atomsd271-52: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC271,SC52
The DISTANCE action with label d271-52 calculates the following quantities:
 Quantity   
 Description  
d271-52.value
the DISTANCE between this pair of atomsd192-271-path: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p1.sss,d192-271 FUNCthe function you wish to evaluate=y+(0.0045*(x^2))-1.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label d192-271-path calculates the following quantities:
 Quantity   
 Description  
d192-271-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=d192-271-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

#YY
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=41338-123566:4    #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=4362,3512,1533 #IsoLeu100 Cb, Leu220 Cgamma, Tyr271 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 coordinationcon192: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC192 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC271 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 con192 calculates the following quantities:
 Quantity   
 Description  
con192.value
the value of the coordinationyywoprod: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=yywo,con192 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,con192 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

#DRY
The CUSTOM action with label yywosum calculates the following quantities:
 Quantity   
 Description  
yywosum.value
an arbitrary functionSC114: 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=1768,1771,1772,1774,1776,1777,1779,1781
The CENTER action with label SC114 calculates the following quantities:
 Quantity   
 Description  
SC114.value
the position of the center of massSC103: 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=1580,1583,1584,1585
The CENTER action with label SC103 calculates the following quantities:
 Quantity   
 Description  
SC103.value
the position of the center of massSC104: 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=1592,1595,1598,1601,1603,1604,1607
The CENTER action with label SC104 calculates the following quantities:
 Quantity   
 Description  
SC104.value
the position of the center of massSC213: 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=3389,3392,3395,3396,3397
The CENTER action with label SC213 calculates the following quantities:
 Quantity   
 Description  
SC213.value
the position of the center of massSC108: 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=1666,1668,1672,1675
The CENTER action with label SC108 calculates the following quantities:
 Quantity   
 Description  
SC108.value
the position of the center of massSC217: 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=3453,3456,3458,3462
The CENTER action with label SC217 calculates the following quantities:
 Quantity   
 Description  
SC217.value
the position of the center of massd103-114: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC103,SC114
The DISTANCE action with label d103-114 calculates the following quantities:
 Quantity   
 Description  
d103-114.value
the DISTANCE between this pair of atomsd104-213: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC104,SC213
The DISTANCE action with label d104-213 calculates the following quantities:
 Quantity   
 Description  
d104-213.value
the DISTANCE between this pair of atomsd108-217: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC108,SC217

The DISTANCE action with label d108-217 calculates the following quantities:
 Quantity   
 Description  
d108-217.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 somethingOPES_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_RFILE=compressed0.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