Project ID: plumID:22.026
Source: Silica_peptoid_PB/ncp/plumed.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsMOLTYPE=proteinwhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleSTRUCTURE=Ncp6.pdba file in pdb format containing a reference structure
bb:COMCalculate the center of mass for a group of atoms. More detailsATOMS=2929,2930,2933,2934,2952,2953,2954,2955,2956,2957,2958,2959,2962,2963,2981,2982,2985,2986,3004,3005,3008,3009,3027,3028,3031,3032,3050,3051,3054,3055,3073,3074,3075the list of atoms which are involved the virtual atom's definition
U1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=2935-2951 U2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=2964-2980 U3:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=2987-3003 U4:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3010-3026 U5:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3033-3049 U6:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=3056-3072the list of atoms which are involved the virtual atom's definition
surf:COMCalculate the center of mass for a group of atoms. More detailsATOMS=78,177,385,439,459,497,570,601,634,637,640,643,644,648,653,660,662,684,709,734,795,898,1036,1041,1110,1184,1222,1295,1328,1365,1368,1371,1373,1376,1377,1382,1389,1412,1438,1521,1620,1759,1829,1883,1903,1941,2014,2042,2046,2079,2082,2085,2087,2089,2093,2098,2105,2106,2107,2128,2153,2156,2183,2244,2347,2490,2560,2614,2634,2672,2745,2778,2815,2818,2821,2823,2826,2827,2832,2838,2861,2886,2892,2908the list of atoms which are involved the virtual atom's definition
dbb:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,bbthe pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdU1:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,U1the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdU2:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,U2the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdU3:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,U3the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdU4:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,U4the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdU5:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,U5the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdU6:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=surf,U6the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dbb.zthe arguments on which the bias is actingAT=4.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_bba label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dU1.zthe arguments on which the bias is actingAT=4.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_U1a label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dU2.zthe arguments on which the bias is actingAT=4.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_U2a label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dU3.zthe arguments on which the bias is actingAT=4.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_U3a label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dU4.zthe arguments on which the bias is actingAT=4.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_U4a label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dU5.zthe arguments on which the bias is actingAT=4.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_U5a label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dU6.zthe arguments on which the bias is actingAT=4.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_U6a label for the action so that its output can be referenced in the input to other actionsGYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=2929-3081the group of atoms that you are calculating the Gyration Tensor forLABEL=rga label for the action so that its output can be referenced in the input to other actionsPBMETAD...Used to performed Parallel Bias metadynamics. More detailsWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRARG=dbb.z,dU1.z,dU2.z,dU3.z,dU4.z,dU5.z,dU6.z,rgthe input for this action is the scalar output from one or more other actionsSIGMA=200.0the widths of the Gaussian hillsADAPTIVE=DIFFuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeSIGMA_MIN=0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MAX=1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.5the upper bounds for the sigmas (in CV units) when using adaptive hillsHEIGHT=1.2 #kJ/molthe height of the Gaussian hills, one for all biasesPACE=500the frequency for hill addition, one for all biasesBIASFACTOR=25 # Sqrt[cv]*8use well tempered metadynamics with this bias factor, one for all biasesTEMP=300.0the system temperature - this is only needed if you are doing well-tempered metadynamicsLABEL=PBMETADa label for the action so that its output can be referenced in the input to other actionsGRID_MIN=-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,0.0the lower bounds for the gridGRID_MAX=5.5,5.5,5.5,5.5,5.5,5.5,5.5,4.0the upper bounds for the gridFILE=../HILLS.dbb,../HILLS.dU1,../HILLS.dU2,../HILLS.dU3,../HILLS.dU4,../HILLS.dU5,../HILLS.dU6,../HILLS.rg ... PBMETADfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not foundPrint quantities to a file. More detailsARG=dbb.z,dU1.z,dU2.z,dU3.z,dU4.z,dU5.z,dU6.z,rg,PBMETAD.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities