Project ID: plumID:23.023
Source: surface_files/plumed.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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## RESTART ## ENERGY LABEL=energy
# all N, CA, C, O atoms bb:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11717,11718,11719,11728,11731,11732,11733,11742,11745,11746,11747,11764,11767,11768,11769,11786,11789,11790,11791,11800,11803,11804,11805,11813,11816,11817,11818,11827,11830,11831,11832,11851,11854,11855,11856,11865,11868,11869,11870,11878,11881,11882,11883,11892,11895,11896,11897,11914,11917,11918,11919,11927,11930,11931,11932,11941,11944,11945,11946,11963,11966,11967,11968,11984,11987,11988,11989,12005,12008,12009,12010,12024,12027,12028,12029,12043,12046,12047,12048the list of atoms which are involved the virtual atom's definition
# Head Groups: CB + on head:COMCalculate the center of mass for a group of atoms. More detailsATOMS=11713-11718 ser1:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11720-11727 ser2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11734-11741 lys1:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11748-11763 lys2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11770-11785 ser3:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11792-11799 gly1:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11806-11812 ser4:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11819-11826 tyr1:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11833-11850 ser5:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11857-11864 gly2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11871-11877 ser6:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11884-11891 lys3:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11898-11913 gly3:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11920-11926 ser7:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11933-11940 lys4:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11947-11962 arg1:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11969-11983 arg2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=11990-12004 ile1:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=12011-12023 leu1:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=12030-12042the list of atoms which are involved the virtual atom's definition
top_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 definition
dbb:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,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 labelNOPBCdhead:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,headthe pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdser1:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,ser1the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdser2:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,ser2the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdlys1:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,lys1the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdlys2:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,lys2the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdser3:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,ser3the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdgly1:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,gly1the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdser4:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,ser4the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdtyr1:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,tyr1the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdser5:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,ser5the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdgly2:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,gly2the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdser6:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,ser6the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdlys3:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,lys3the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdgly3:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,gly3the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdser7:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,ser7the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdlys4:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,lys4the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdarg1:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,arg1the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdarg2:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,arg2the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdile1:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,ile1the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelNOPBCdleu1:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=top_oh,leu1the 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=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dbba 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=dhead.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dheada 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=dser1.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dser1a 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=dser2.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dser2a 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=dlys1.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dlys1a 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=dlys2.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dlys2a 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=dser3.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dser3a 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=dgly1.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dgly1a 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=dser4.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dser4a 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=dtyr1.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dtyr1a 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=dser5.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dser5a 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=dgly2.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dgly2a 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=dser6.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dser6a 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=dlys3.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dlys3a 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=dgly3.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dgly3a 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=dser7.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dser7a 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=dlys4.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dlys4a 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=darg1.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_darg1a 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=darg2.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_darg2a 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=dile1.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dile1a 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=dleu1.zthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwall_dleu1a label for the action so that its output can be referenced in the input to other actions
# Radius of Gyration: All atoms in chainGYRATIONCalculate 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=11713-12050the 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,dhead.z,dser1.z,dser2.z,dlys1.z,dlys2.z,dser3.z,dgly1.z,dser4.z,dtyr1.z,dser5.z,dgly2.z,dser6.z,dlys3.z,dgly3.z,dser7.z,dlys4.z,darg1.z,darg2.z,dile1.z,dleu1.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=0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MAX=0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4the 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=35 # 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,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,0.0the lower bounds for the gridGRID_MAX=6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.0the upper bounds for the gridFILE=../HILLS.dbb,../HILLS.dhead,../HILLS.dser1,../HILLS.dser2,../HILLS.dlys1,../HILLS.dlys2,../HILLS.dser3,../HILLS.dgly1,../HILLS.dser4,../HILLS.dtyr1,../HILLS.dser5,../HILLS.dgly2,../HILLS.dser6,../HILLS.dlys3,../HILLS.dgly3,../HILLS.dser7,../HILLS.dlys4,../HILLS.darg1,../HILLS.darg2,../HILLS.dile1,../HILLS.dleu1,../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=PBMETAD.bias,dbb.z,dhead.z,dser1.z,dser2.z,dlys1.z,dlys2.z,dser3.z,dgly1.z,dser4.z,dtyr1.z,dser5.z,dgly2.z,dser6.z,dlys3.z,dgly3.z,dser7.z,dlys4.z,darg1.z,darg2.z,dile1.z,dleu1.z,rgthe 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