PLUMED-NEST-TEST-SITE by plumed-nest

Project ID: plumID:25.007
Source: plumed_M5G0+MII_steer_theta.dat
Originally used with PLUMED version: 2.8
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
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phi1_2The TORSION action with label phi1_2 calculates the following quantities: Quantity    Type    Description  
phi1_2 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16217,16215,16214,16204
psi1_2The TORSION action with label psi1_2 calculates the following quantities: Quantity    Type    Description  
psi1_2 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16215,16214,16204,16200
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phi2_3The TORSION action with label phi2_3 calculates the following quantities: Quantity    Type    Description  
phi2_3 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16251,16235,16223,16220
psi2_3The TORSION action with label psi2_3 calculates the following quantities: Quantity    Type    Description  
psi2_3 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16235,16223,16220,16218
omega2_3The TORSION action with label omega2_3 calculates the following quantities: Quantity    Type    Description  
omega2_3 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16223,16220,16218,16224
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phi3_4The TORSION action with label phi3_4 calculates the following quantities: Quantity    Type    Description  
phi3_4 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16270,16255,16254,16241
psi3_4The TORSION action with label psi3_4 calculates the following quantities: Quantity    Type    Description  
psi3_4 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16255,16254,16241,16237
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phi3_5The TORSION action with label phi3_5 calculates the following quantities: Quantity    Type    Description  
phi3_5 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16292,16277,16250,16247
psi3_5The TORSION action with label psi3_5 calculates the following quantities: Quantity    Type    Description  
psi3_5 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16277,16250,16247,16245
omega3_5The TORSION action with label omega3_5 calculates the following quantities: Quantity    Type    Description  
omega3_5 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16250,16247,16245,16243
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phi2_6The TORSION action with label phi2_6 calculates the following quantities: Quantity    Type    Description  
phi2_6 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16314,16299,16234,16228
psi2_6The TORSION action with label psi2_6 calculates the following quantities: Quantity    Type    Description  
psi2_6 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16299,16234,16228,16230
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phi6_7The TORSION action with label phi6_7 calculates the following quantities: Quantity    Type    Description  
phi6_7 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16322,16320,16319,16301
psi6_7The TORSION action with label psi6_7 calculates the following quantities: Quantity    Type    Description  
psi6_7 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16320,16319,16301,16299
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puck1The PUCKERING action with label puck1 calculates the following quantities: Quantity    Type    Description  
puck1.qx scalar Cartesian component x (6 membered rings)
puck1.qy scalar Cartesian component y (6 membered rings)
puck1.qz scalar Cartesian component z (6 membered rings)
puck1.phi scalar Pseudorotation phase (6 membered rings)
puck1.theta scalar Theta angle (6 membered rings)
puck1.amplitude scalar Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=16213,16188,16190,16200,16204,16206
puck2The PUCKERING action with label puck2 calculates the following quantities: Quantity    Type    Description  
puck2.qx scalar Cartesian component x (6 membered rings)
puck2.qy scalar Cartesian component y (6 membered rings)
puck2.qz scalar Cartesian component z (6 membered rings)
puck2.phi scalar Pseudorotation phase (6 membered rings)
puck2.theta scalar Theta angle (6 membered rings)
puck2.amplitude scalar Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=16217,16215,16230,16228,16224,16218
puck3The PUCKERING action with label puck3 calculates the following quantities: Quantity    Type    Description  
puck3.qx scalar Cartesian component x (6 membered rings)
puck3.qy scalar Cartesian component y (6 membered rings)
puck3.qz scalar Cartesian component z (6 membered rings)
puck3.phi scalar Pseudorotation phase (6 membered rings)
puck3.theta scalar Theta angle (6 membered rings)
puck3.amplitude scalar Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=16251,16235,16237,16241,16243,16245
puck4The PUCKERING action with label puck4 calculates the following quantities: Quantity    Type    Description  
puck4.qx scalar Cartesian component x (6 membered rings)
puck4.qy scalar Cartesian component y (6 membered rings)
puck4.qz scalar Cartesian component z (6 membered rings)
puck4.phi scalar Pseudorotation phase (6 membered rings)
puck4.theta scalar Theta angle (6 membered rings)
puck4.amplitude scalar Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=16270,16255,16257,16259,16261,16263
puck5The PUCKERING action with label puck5 calculates the following quantities: Quantity    Type    Description  
puck5.qx scalar Cartesian component x (6 membered rings)
puck5.qy scalar Cartesian component y (6 membered rings)
puck5.qz scalar Cartesian component z (6 membered rings)
puck5.phi scalar Pseudorotation phase (6 membered rings)
puck5.theta scalar Theta angle (6 membered rings)
puck5.amplitude scalar Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=16292,16277,16279,16281,16283,16285
puck6The PUCKERING action with label puck6 calculates the following quantities: Quantity    Type    Description  
puck6.qx scalar Cartesian component x (6 membered rings)
puck6.qy scalar Cartesian component y (6 membered rings)
puck6.qz scalar Cartesian component z (6 membered rings)
puck6.phi scalar Pseudorotation phase (6 membered rings)
puck6.theta scalar Theta angle (6 membered rings)
puck6.amplitude scalar Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=16314,16299,16301,16303,16305,16307
puck7The PUCKERING action with label puck7 calculates the following quantities: Quantity    Type    Description  
puck7.qx scalar Cartesian component x (6 membered rings)
puck7.qy scalar Cartesian component y (6 membered rings)
puck7.qz scalar Cartesian component z (6 membered rings)
puck7.phi scalar Pseudorotation phase (6 membered rings)
puck7.theta scalar Theta angle (6 membered rings)
puck7.amplitude scalar Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=16322,16320,16338,16334,16330,16323
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PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=phi1_2,psi1_2,phi2_3,psi2_3,omega2_3,phi3_4,psi3_4,phi3_5,psi3_5,omega3_5,phi2_6,psi2_6,phi6_7,psi6_7 STRIDE the frequency with which the quantities of interest should be output=5000 FILEthe name of the file on which to output these quantities=COLVAR
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The PRINT action with label  calculates somethingPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=puck1.theta,puck2.theta,puck3.theta,puck4.theta,puck5.theta,puck6.theta,puck7.theta,puck1.phi,puck2.phi,puck3.phi,puck4.phi,puck5.phi,puck6.phi,puck7.phi STRIDE the frequency with which the quantities of interest should be output=5000 FILEthe name of the file on which to output these quantities=COLVAR_theta
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# Distances
#Tyr269-Glycan H of OH at C2
Tyr269-HOC2The DISTANCE action with label Tyr269-HOC2 calculates the following quantities: Quantity    Type    Description  
Tyr269-HOC2 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=3939,16297
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#Asp92-Glycan H of OH at C2 and C3
Asp92O1-HOC3The DISTANCE action with label Asp92O1-HOC3 calculates the following quantities: Quantity    Type    Description  
Asp92O1-HOC3 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=1006,16296
Asp92O2-HOC2The DISTANCE action with label Asp92O2-HOC2 calculates the following quantities: Quantity    Type    Description  
Asp92O2-HOC2 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=1007,16298
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#His471-Glycan O of OH at C3
His471-OC3The DISTANCE action with label His471-OC3 calculates the following quantities: Quantity    Type    Description  
His471-OC3 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=7215,16295
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#Asp472-Glycan H of OH at C3 and C4
Asp472-HOC4The DISTANCE action with label Asp472-HOC4 calculates the following quantities: Quantity    Type    Description  
Asp472-HOC4 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=7228,16294
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Asp472-HOC3The DISTANCE action with label Asp472-HOC3 calculates the following quantities: Quantity    Type    Description  
Asp472-HOC3 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=7229,16296
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#Tyr727-Glycan O of OH at C4
Tyr727-OC4The DISTANCE action with label Tyr727-OC4 calculates the following quantities: Quantity    Type    Description  
Tyr727-OC4 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=11250,16293
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#Arg876-Glycan H of OH at C6
Arg876-HOC6The DISTANCE action with label Arg876-HOC6 calculates the following quantities: Quantity    Type    Description  
Arg876-HOC6 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=13561,16291
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#Arg228-Glycan O5
Arg228H1-O5The DISTANCE action with label Arg228H1-O5 calculates the following quantities: Quantity    Type    Description  
Arg228H1-O5 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=3237,16292
Arg228H2-O5The DISTANCE action with label Arg228H2-O5 calculates the following quantities: Quantity    Type    Description  
Arg228H2-O5 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=3238,16292
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#Asp341-Glycan O linkage
Asp341-OThe DISTANCE action with label Asp341-O calculates the following quantities: Quantity    Type    Description  
Asp341-O 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=5077,16250
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#Asp204-Glycan H of OH at C2
Asp204O1-HOC2The DISTANCE action with label Asp204O1-HOC2 calculates the following quantities: Quantity    Type    Description  
Asp204O1-HOC2 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=2841,16298
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## Distances Amino acids - ZN
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ZN-GOHC2The DISTANCE action with label ZN-GOHC2 calculates the following quantities: Quantity    Type    Description  
ZN-GOHC2 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=16348,16297
ZN-GOHC3The DISTANCE action with label ZN-GOHC3 calculates the following quantities: Quantity    Type    Description  
ZN-GOHC3 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=16348,16295
ZN-Asp204The DISTANCE action with label ZN-Asp204 calculates the following quantities: Quantity    Type    Description  
ZN-Asp204 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=16348,2841
ZN-His90The DISTANCE action with label ZN-His90 calculates the following quantities: Quantity    Type    Description  
ZN-His90 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=16348,979
ZN-Asp92The DISTANCE action with label ZN-Asp92 calculates the following quantities: Quantity    Type    Description  
ZN-Asp92 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=16348,1006
ZN-His471The DISTANCE action with label ZN-His471 calculates the following quantities: Quantity    Type    Description  
ZN-His471 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=16348,7215
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#Steered MD
restraintThe MOVINGRESTRAINT action with label restraint calculates the following quantities: Quantity    Type    Description  
restraint.bias scalar the instantaneous value of the bias potential
restraint.force2 scalar the instantaneous value of the squared force due to this bias potential
restraint.puck5.theta_cntr scalar one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _cntr. These quantities give the instantaneous position of the center of the harmonic potential. This particular component measures this quantity for the input CV named puck5.theta
restraint.puck5.theta_work scalar one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _work. These quantities tell the user how much work has been done by the potential in dragging the system along the various colvar axis. This particular component measures this quantity for the input CV named puck5.theta
restraint.puck5.theta_kappa scalar one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _kappa. These quantities tell the user the time dependent value of kappa. This particular component measures this quantity for the input CV named puck5.theta
restraint.work scalar the total work performed changing this restraint: ... 
	MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. This action has hidden defaults. More details
    ARGthe labels of the scalars on which the bias will act=puck5.theta
    AT0ATx is equal to the position of the restraint at time STEPx=0.25  STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0        KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=500    
    AT1ATx is equal to the position of the restraint at time STEPx=0.25  STEP1This keyword appears multiple times as STEPx with x=0,1,2,=250000   KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=500 #0.500 ns
    AT2ATx is equal to the position of the restraint at time STEPx=1.5   STEP2This keyword appears multiple times as STEPx with x=0,1,2,=500000   KAPPA2KAPPAx is equal to the value of the force constants at time STEPx=500 #1.000 ns ramping
    AT3ATx is equal to the position of the restraint at time STEPx=1.5   STEP3This keyword appears multiple times as STEPx with x=0,1,2,=1000000  KAPPA3KAPPAx is equal to the value of the force constants at time STEPx=500 #2.000 ns
    AT4ATx is equal to the position of the restraint at time STEPx=0.25  STEP4This keyword appears multiple times as STEPx with x=0,1,2,=1250000  KAPPA4KAPPAx is equal to the value of the force constants at time STEPx=500 #2.500 ns ramping
    AT5ATx is equal to the position of the restraint at time STEPx=0.25  STEP5This keyword appears multiple times as STEPx with x=0,1,2,=1750000  KAPPA5KAPPAx is equal to the value of the force constants at time STEPx=500 #3.500 ns
    AT6ATx is equal to the position of the restraint at time STEPx=1.5   STEP6This keyword appears multiple times as STEPx with x=0,1,2,=2000000  KAPPA6KAPPAx is equal to the value of the force constants at time STEPx=500 #4.000 ns ramping
    AT7ATx is equal to the position of the restraint at time STEPx=1.5   STEP7This keyword appears multiple times as STEPx with x=0,1,2,=2500000  KAPPA7KAPPAx is equal to the value of the force constants at time STEPx=500 #5.000 ns 
    AT8ATx is equal to the position of the restraint at time STEPx=0.25  STEP8This keyword appears multiple times as STEPx with x=0,1,2,=2750000  KAPPA8KAPPAx is equal to the value of the force constants at time STEPx=500 #5.500 ns ramping
    AT9ATx is equal to the position of the restraint at time STEPx=0.25  STEP9This keyword appears multiple times as STEPx with x=0,1,2,=3000000  KAPPA9KAPPAx is equal to the value of the force constants at time STEPx=500 #6.000 ns 
...
restraint: ... 
	MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. This action uses the defaults shown here. More details
    ARGthe labels of the scalars on which the bias will act=puck5.theta
    AT0ATx is equal to the position of the restraint at time STEPx=0.25  STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0        KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=500    
    AT1ATx is equal to the position of the restraint at time STEPx=0.25  STEP1This keyword appears multiple times as STEPx with x=0,1,2,=250000   KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=500 #0.500 ns
    AT2ATx is equal to the position of the restraint at time STEPx=1.5   STEP2This keyword appears multiple times as STEPx with x=0,1,2,=500000   KAPPA2KAPPAx is equal to the value of the force constants at time STEPx=500 #1.000 ns ramping
    AT3ATx is equal to the position of the restraint at time STEPx=1.5   STEP3This keyword appears multiple times as STEPx with x=0,1,2,=1000000  KAPPA3KAPPAx is equal to the value of the force constants at time STEPx=500 #2.000 ns
    AT4ATx is equal to the position of the restraint at time STEPx=0.25  STEP4This keyword appears multiple times as STEPx with x=0,1,2,=1250000  KAPPA4KAPPAx is equal to the value of the force constants at time STEPx=500 #2.500 ns ramping
    AT5ATx is equal to the position of the restraint at time STEPx=0.25  STEP5This keyword appears multiple times as STEPx with x=0,1,2,=1750000  KAPPA5KAPPAx is equal to the value of the force constants at time STEPx=500 #3.500 ns
    AT6ATx is equal to the position of the restraint at time STEPx=1.5   STEP6This keyword appears multiple times as STEPx with x=0,1,2,=2000000  KAPPA6KAPPAx is equal to the value of the force constants at time STEPx=500 #4.000 ns ramping
    AT7ATx is equal to the position of the restraint at time STEPx=1.5   STEP7This keyword appears multiple times as STEPx with x=0,1,2,=2500000  KAPPA7KAPPAx is equal to the value of the force constants at time STEPx=500 #5.000 ns 
    AT8ATx is equal to the position of the restraint at time STEPx=0.25  STEP8This keyword appears multiple times as STEPx with x=0,1,2,=2750000  KAPPA8KAPPAx is equal to the value of the force constants at time STEPx=500 #5.500 ns ramping
    AT9ATx is equal to the position of the restraint at time STEPx=0.25  STEP9This keyword appears multiple times as STEPx with x=0,1,2,=3000000  KAPPA9KAPPAx is equal to the value of the force constants at time STEPx=500 #6.000 ns 
 VERSE Tells plumed whether the restraint is only acting for CV larger (U) or smaller (L) than the restraint or whether it is acting on both sides (B)=B
...
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PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=Tyr269-HOC2,Asp92O1-HOC3,Asp92O2-HOC2,His471-OC3,Asp472-HOC4,Asp472-HOC3,Tyr727-OC4,Arg876-HOC6,Arg228H1-O5,Arg228H2-O5,Asp341-O,Asp204O1-HOC2,ZN-GOHC2,ZN-GOHC3,ZN-Asp204,ZN-His90,ZN-Asp92,ZN-His471,restraint.* FILEthe name of the file on which to output these quantities=COLVAR_coordination STRIDE the frequency with which the quantities of interest should be output=5000
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Quantity	Type	Description
phi1_2	scalar	the TORSION involving these atoms
PLUMED-NEST-TEST-SITE

The public repository of the PLUMED consortium
