**Project ID:** plumID:21.022

**Source:** SiNP_Car9/plumed.dat

**Originally used with PLUMED version:** 2.4

**Stable:** zipped raw stdout - zipped raw stderr - stderr

**Master:** zipped raw stdout - zipped raw stderr - stderr

## RESTARTMOLINFOThis 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=car9_ACE_NME.pdba file in pdb format containing a reference structureENERGYCalculate the total potential energy of the simulation box. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsenergyncap:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11713-11718the list of atoms which are involved the virtual atom's definitionccap:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11914-11919the list of atoms which are involved the virtual atom's definitionbb:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11717,11718,11719,11729,11730,11731,11740,11741,11742,11750,11751,11752,11774,11775,11776,11781,11782,11783,11801,11802,11803,11823,11824,11825,11845,11846,11847,11859,11860,11861,11866,11867,11868,11888,11889,11890,11912,11913,11914the list of atoms which are involved the virtual atom's definitionasp:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11720-11728the list of atoms which are involved the virtual atom's definitionser:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11732-11739the list of atoms which are involved the virtual atom's definitionala:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11743-11749the list of atoms which are involved the virtual atom's definitionarg:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11753-11773the list of atoms which are involved the virtual atom's definitiongly:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11777-11780the list of atoms which are involved the virtual atom's definitionphe:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11784-11800the list of atoms which are involved the virtual atom's definitionlys:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11804-11822the list of atoms which are involved the virtual atom's definitionlys2:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11826-11844the list of atoms which are involved the virtual atom's definitionpro:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11848-11858the list of atoms which are involved the virtual atom's definitiongly2:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11862-11865the list of atoms which are involved the virtual atom's definitionlys3:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11869-11887the list of atoms which are involved the virtual atom's definitionarg2:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11891-11911the list of atoms which are involved the virtual atom's definitiontop_oh:COMCalculate the center of mass for a group of atoms. More detailsATOMS=78,177,385,439,459,497,570,601,634,637,640,643,644,648,653,660,662,684,709,734,795,898,1036,1041,1110,1184,1222,1295,1328,1365,1368,1371,1373,1376,1377,1382,1389,1412,1438,1521,1620,1759,1829,1883,1903,1941,2014,2042,2046,2079,2082,2085,2087,2089,2093,2098,2105,2106,2107,2128,2153,2156,2183,2244,2347,2490,2560,2614,2634,2672,2745,2778,2815,2818,2821,2823,2826,2827,2832,2838,2861,2886,2892,2908,3006,3105,3313,3367,3387,3425,3498,3529,3562,3565,3568,3571,3572,3576,3581,3588,3590,3612,3637,3662,3723,3826,3964,3969,4038,4112,4150,4223,4256,4293,4296,4299,4301,4304,4305,4310,4317,4340,4366,4449,4548,4687,4757,4811,4831,4869,4942,4970,4974,5007,5010,5013,5015,5017,5021,5026,5033,5034,5035,5056,5081,5084,5111,5172,5275,5418,5488,5542,5562,5600,5673,5706,5743,5746,5749,5751,5754,5755,5760,5766,5789,5814,5820,5836,5934,6033,6241,6295,6315,6353,6426,6457,6490,6493,6496,6499,6500,6504,6509,6516,6518,6540,6565,6590,6651,6754,6892,6897,6966,7040,7078,7151,7184,7221,7224,7227,7229,7232,7233,7238,7245,7268,7294,7377,7476,7615,7685,7739,7759,7797,7870,7898,7902,7935,7938,7941,7943,7945,7949,7954,7961,7962,7963,7984,8009,8012,8039,8100,8203,8346,8416,8470,8490,8528,8601,8634,8671,8674,8677,8679,8682,8683,8688,8694,8717,8742,8748,8764,8862,8961,9169,9223,9243,9281,9354,9385,9418,9421,9424,9427,9428,9432,9437,9444,9446,9468,9493,9518,9579,9682,9820,9825,9894,9968,10006,10079,10112,10149,10152,10155,10157,10160,10161,10166,10173,10196,10222,10305,10404,10543,10613,10667,10687,10725,10798,10826,10830,10863,10866,10869,10871,10873,10877,10882,10889,10890,10891,10912,10937,10940,10967,11028,11131,11274,11344,11398,11418,11456,11529,11562,11599,11602,11605,11607,11610,11611,11616,11622,11645,11670,11676,11692the list of atoms which are involved the virtual atom's definitiondcaps:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenncap,ccapdncap:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,ncapCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdccap:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,ccapCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdbb:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,bbCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdasp:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,aspCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdser:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,serCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdala:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,alaCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdarg:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,argCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdgly:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,glyCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdphe:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,pheCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdlys:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,lysCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdlys2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,lys2COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdpro:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,proCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdgly2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,gly2COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdlys3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,lys3COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesdarg2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweentop_oh,arg2COMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCignore the periodic boundary conditions when calculating distancesLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdcapsAT=0.8the positions of the wallKAPPA=100000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsdcaps_minUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdcapsAT=1.8the positions of the wallKAPPA=100000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsdcaps_maxLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdncap.zAT=0.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsdncap_minLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdccap.zAT=0.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsdccap_minUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdbb.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dbbUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdasp.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_daspUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdser.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dserUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdala.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dalaUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdarg.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dargUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdgly.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dglyUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdphe.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dpheUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdlys.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dlysUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdlys2.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dlys2UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdpro.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dproUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdgly2.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dgly2UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdlys3.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_dlys3UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdarg2.zAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_darg2GYRATIONCalculate 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=11713-11919the group of atoms that you are calculating the Gyration Tensor forLABEL=a label for the action so that its output can be referenced in the input to other actionsrgPBMETAD...Used to performed Parallel Bias metadynamics. More detailsWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRARG=the input for this action is the scalar output from one or more other actionsdbb.z,dasp.z,dser.z,dala.z,darg.z,dgly.z,dphe.z,dlys.z,dlys2.z,dpro.z,dgly2.z,dlys3.z,darg2.z,rgSIGMA=0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02the widths of the Gaussian hillsHEIGHT=1.2 #kJ/molthe height of the Gaussian hills, one for all biasesPACE=1000the frequency for hill addition, one for all biasesBIASFACTOR=20use well tempered metadynamics with this bias factor, one for all biasesTEMP=298.0the system temperature - this is only needed if you are doing well-tempered metadynamicsLABEL=a label for the action so that its output can be referenced in the input to other actionsPBMETADGRID_MIN=-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,0.0the lower bounds for the gridGRID_MAX=9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,8the upper bounds for the gridFILE=HILLS.dbb,HILLS.dasp,HILLS.dser,HILLS.dala,HILLS.darg,HILLS.dgly,HILLS.dphe,HILLS.dlys,HILLS.dlys2,HILLS.dpro,HILLS.dgly2,HILLS.dlys3,HILLS.darg2,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=the input for this action is the scalar output from one or more other actionsdcaps,dbb.z,dncap.z,dccap.z,dasp.z,dser.z,dala.z,darg.z,dgly.z,dphe.z,dlys.z,dlys2.z,dpro.z,dgly2.z,dlys3.z,darg2.z,rg,energy,PBMETAD.biasSTRIDE=500the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities