Project ID: plumID:25.007
Source: plumed_M5G0.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
 |
 |
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=reference_M5G0.pdb # selection of torsion angles and rings # phi1_2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-2the O5 atom in residue 2. Click here for more information. ,@C1-2the C1 atom in residue 2. Click here for more information. ,@O4-1the O4 atom in residue 1. Click here for more information. ,@C4-1the C4 atom in residue 1. Click here for more information. psi1_2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-2the C1 atom in residue 2. Click here for more information. ,@O4-1the O4 atom in residue 1. Click here for more information. ,@C4-1the C4 atom in residue 1. Click here for more information. ,@C3-1the C3 atom in residue 1. Click here for more information. # phi2_3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-3the O5 atom in residue 3. Click here for more information. ,@C1-3the C1 atom in residue 3. Click here for more information. ,@O6-2the O6 atom in residue 2. Click here for more information. ,@C6-2the C6 atom in residue 2. Click here for more information. psi2_3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-3the C1 atom in residue 3. Click here for more information. ,@O6-2the O6 atom in residue 2. Click here for more information. ,@C6-2the C6 atom in residue 2. Click here for more information. ,@C5-2the C5 atom in residue 2. Click here for more information. omega2_3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O6-2the O6 atom in residue 2. Click here for more information. ,@C6-2the C6 atom in residue 2. Click here for more information. ,@C5-2the C5 atom in residue 2. Click here for more information. ,@O5-2the O5 atom in residue 2. Click here for more information. # phi3_4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-4the O5 atom in residue 4. Click here for more information. ,@C1-4the C1 atom in residue 4. Click here for more information. ,@O3-3the O3 atom in residue 3. Click here for more information. ,@C3-3the C3 atom in residue 3. Click here for more information. psi3_4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-4the C1 atom in residue 4. Click here for more information. ,@O3-3the O3 atom in residue 3. Click here for more information. ,@C3-3the C3 atom in residue 3. Click here for more information. ,@C2-3the C2 atom in residue 3. Click here for more information. # phi3_5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-5the O5 atom in residue 5. Click here for more information. ,@C1-5the C1 atom in residue 5. Click here for more information. ,@O6-3the O6 atom in residue 3. Click here for more information. ,@C6-3the C6 atom in residue 3. Click here for more information. psi3_5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-5the C1 atom in residue 5. Click here for more information. ,@O6-3the O6 atom in residue 3. Click here for more information. ,@C6-3the C6 atom in residue 3. Click here for more information. ,@C5-3the C5 atom in residue 3. Click here for more information. omega3_5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O6-3the O6 atom in residue 3. Click here for more information. ,@C6-3the C6 atom in residue 3. Click here for more information. ,@C5-3the C5 atom in residue 3. Click here for more information. ,@O5-3the O5 atom in residue 3. Click here for more information. # phi2_6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-6the O5 atom in residue 6. Click here for more information. ,@C1-6the C1 atom in residue 6. Click here for more information. ,@O3-2the O3 atom in residue 2. Click here for more information. ,@C3-2the C3 atom in residue 2. Click here for more information. psi2_6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-6the C1 atom in residue 6. Click here for more information. ,@O3-2the O3 atom in residue 2. Click here for more information. ,@C3-2the C3 atom in residue 2. Click here for more information. ,@C2-2the C2 atom in residue 2. Click here for more information. # phi6_7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-7the O5 atom in residue 7. Click here for more information. ,@C1-7the C1 atom in residue 7. Click here for more information. ,@O2-6the O2 atom in residue 6. Click here for more information. ,@C2-6the C2 atom in residue 6. Click here for more information. psi6_7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-7the C1 atom in residue 7. Click here for more information. ,@O2-6the O2 atom in residue 6. Click here for more information. ,@C2-6the C2 atom in residue 6. Click here for more information. ,@C1-6the C1 atom in residue 6. Click here for more information. # puck1: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-1the O5 atom in residue 1. Click here for more information. ,@C1-1the C1 atom in residue 1. Click here for more information. ,@C2-1the C2 atom in residue 1. Click here for more information. ,@C3-1the C3 atom in residue 1. Click here for more information. ,@C4-1the C4 atom in residue 1. Click here for more information. ,@C5-1the C5 atom in residue 1. Click here for more information. puck2: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-2the O5 atom in residue 2. Click here for more information. ,@C1-2the C1 atom in residue 2. Click here for more information. ,@C2-2the C2 atom in residue 2. Click here for more information. ,@C3-2the C3 atom in residue 2. Click here for more information. ,@C4-2the C4 atom in residue 2. Click here for more information. ,@C5-2the C5 atom in residue 2. Click here for more information. puck3: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-3the O5 atom in residue 3. Click here for more information. ,@C1-3the C1 atom in residue 3. Click here for more information. ,@C2-3the C2 atom in residue 3. Click here for more information. ,@C3-3the C3 atom in residue 3. Click here for more information. ,@C4-3the C4 atom in residue 3. Click here for more information. ,@C5-3the C5 atom in residue 3. Click here for more information. puck4: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-4the O5 atom in residue 4. Click here for more information. ,@C1-4the C1 atom in residue 4. Click here for more information. ,@C2-4the C2 atom in residue 4. Click here for more information. ,@C3-4the C3 atom in residue 4. Click here for more information. ,@C4-4the C4 atom in residue 4. Click here for more information. ,@C5-4the C5 atom in residue 4. Click here for more information. puck5: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-5the O5 atom in residue 5. Click here for more information. ,@C1-5the C1 atom in residue 5. Click here for more information. ,@C2-5the C2 atom in residue 5. Click here for more information. ,@C3-5the C3 atom in residue 5. Click here for more information. ,@C4-5the C4 atom in residue 5. Click here for more information. ,@C5-5the C5 atom in residue 5. Click here for more information. puck6: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-6the O5 atom in residue 6. Click here for more information. ,@C1-6the C1 atom in residue 6. Click here for more information. ,@C2-6the C2 atom in residue 6. Click here for more information. ,@C3-6the C3 atom in residue 6. Click here for more information. ,@C4-6the C4 atom in residue 6. Click here for more information. ,@C5-6the C5 atom in residue 6. Click here for more information. puck7: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-7the O5 atom in residue 7. Click here for more information. ,@C1-7the C1 atom in residue 7. Click here for more information. ,@C2-7the C2 atom in residue 7. Click here for more information. ,@C3-7the C3 atom in residue 7. Click here for more information. ,@C4-7the C4 atom in residue 7. Click here for more information. ,@C5-7the C5 atom in residue 7. Click here for more information. # #Metadynamics: HEIGHTS=(k*deltaT*pace*timestep)/tau # 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 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=4000 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=4000 FILEthe name of the file on which to output these quantities=COLVAR_theta #