Project ID: plumID:25.007
Source: plumed_M5G0+MII.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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RESTARTActivate restart. More details # phi1_2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16217,16215,16214,16204 psi1_2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16215,16214,16204,16200 # phi2_3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16251,16235,16223,16220 psi2_3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16235,16223,16220,16218 omega2_3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16223,16220,16218,16224 # phi3_4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16270,16255,16254,16241 psi3_4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16255,16254,16241,16237 # phi3_5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16292,16277,16250,16247 psi3_5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16277,16250,16247,16245 omega3_5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16250,16247,16245,16243 # phi2_6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16314,16299,16234,16228 psi2_6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16299,16234,16228,16230 # phi6_7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16322,16320,16319,16301 psi6_7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16320,16319,16301,16299 # puck1: 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 puck2: 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 puck3: 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 puck4: 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 puck5: 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 puck6: 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 puck7: 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 # metaD_phi1_2: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi1_2 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_phi1_2 metaD_psi1_2: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi1_2 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_psi1_2 # metaD_phi2_3: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi2_3 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_phi2_3 metaD_psi2_3: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi2_3 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_psi2_3 metaD_omega2_3: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=omega2_3 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_omega2_3 # metaD_phi3_4: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi3_4 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_phi3_4 metaD_psi3_4: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi3_4 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_psi3_4 # metaD_phi3_5: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi3_5 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_phi3_5 metaD_psi3_5: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi3_5 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_psi3_5 metaD_omega3_5: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=omega3_5 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_omega3_5 # metaD_phi2_6: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi2_6 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_phi2_6 metaD_psi2_6: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi2_6 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_psi2_6 # metaD_phi6_7: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi6_7 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_phi6_7 metaD_psi6_7: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi6_7 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist of bias factors for all the replicas=1,1.12688,1.26985,1.43097,1.61253,1.81712,2.04767,2.30748,2.60024,2.93016,3.30193,3.72086,4.19296,4.72497,5.32444,6 FILE a file in which the list of added hills is stored=HILLS_psi6_7 # 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 # PRINTPrint 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 # PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=metaD_phi1_2.bias,metaD_psi1_2.bias,metaD_phi2_3.bias,metaD_psi2_3.bias,metaD_omega2_3.bias,metaD_phi3_4.bias,metaD_psi3_4.bias,metaD_phi3_5.bias,metaD_psi3_5.bias,metaD_omega3_5.bias,metaD_phi2_6.bias,metaD_psi2_6.bias,metaD_phi6_7.bias,metaD_psi6_7.bias 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_bias # # Distances #Tyr269-Glycan H of OH at C2 Tyr269-HOC2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3939,16297 ## #Asp92-Glycan H of OH at C2 and C3 Asp92O1-HOC3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1006,16296 Asp92O2-HOC2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1007,16298 ## #His471-Glycan O of OH at C3 His471-OC3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7215,16295 ## #Asp472-Glycan H of OH at C3 and C4 Asp472-HOC4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7228,16294 # Asp472-HOC3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7229,16296 # #Tyr727-Glycan O of OH at C4 Tyr727-OC4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11250,16293 # #Arg876-Glycan H of OH at C6 Arg876-HOC6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=13561,16291 # #Arg228-Glycan O5 Arg228H1-O5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3237,16292 Arg228H2-O5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3238,16292 # #Asp341-Glycan O linkage Asp341-O: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5077,16250 # #Asp204-Glycan H of OH at C2 Asp204O1-HOC2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2841,16298 # ## Distances Amino acids - ZN # ZN-GOHC2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16348,16297 ZN-GOHC3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16348,16295 ZN-Asp204: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16348,2841 ZN-His90: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16348,979 ZN-Asp92: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16348,1006 ZN-His471: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16348,7215 # Required to keep the ion correctly positioned also in higher replica Zn_restraint: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=ZN-His471,ZN-His90,ZN-GOHC2,ZN-GOHC3 ATthe position of the restraint=0.22,0.5,0.4,0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=150,150,150,150 # 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,*.bias 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