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
Click on the labels of the actions for more information on what each action computes
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## RESTART
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=car9_ACE_NME.pdb ENERGYCalculate the total potential energy of the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=energy
ncap: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11713-11718 ccap: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11914-11919 bb: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11717,11718,11719,11729,11730,11731,11740,11741,11742,11750,11751,11752,11774,11775,11776,11781,11782,11783,11801,11802,11803,11823,11824,11825,11845,11846,11847,11859,11860,11861,11866,11867,11868,11888,11889,11890,11912,11913,11914 asp: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11720-11728 ser: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11732-11739 ala: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11743-11749 arg: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11753-11773 gly: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11777-11780 phe: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11784-11800 lys: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11804-11822 lys2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11826-11844 pro: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11848-11858 gly2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11862-11865 lys3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11869-11887 arg2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11891-11911 top_oh: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=78,177,385,439,459,497,570,601,634,637,640,643,644,648,653,660,662,684,709,734,795,898,1036,1041,1110,1184,1222,1295,1328,1365,1368,1371,1373,1376,1377,1382,1389,1412,1438,1521,1620,1759,1829,1883,1903,1941,2014,2042,2046,2079,2082,2085,2087,2089,2093,2098,2105,2106,2107,2128,2153,2156,2183,2244,2347,2490,2560,2614,2634,2672,2745,2778,2815,2818,2821,2823,2826,2827,2832,2838,2861,2886,2892,2908,3006,3105,3313,3367,3387,3425,3498,3529,3562,3565,3568,3571,3572,3576,3581,3588,3590,3612,3637,3662,3723,3826,3964,3969,4038,4112,4150,4223,4256,4293,4296,4299,4301,4304,4305,4310,4317,4340,4366,4449,4548,4687,4757,4811,4831,4869,4942,4970,4974,5007,5010,5013,5015,5017,5021,5026,5033,5034,5035,5056,5081,5084,5111,5172,5275,5418,5488,5542,5562,5600,5673,5706,5743,5746,5749,5751,5754,5755,5760,5766,5789,5814,5820,5836,5934,6033,6241,6295,6315,6353,6426,6457,6490,6493,6496,6499,6500,6504,6509,6516,6518,6540,6565,6590,6651,6754,6892,6897,6966,7040,7078,7151,7184,7221,7224,7227,7229,7232,7233,7238,7245,7268,7294,7377,7476,7615,7685,7739,7759,7797,7870,7898,7902,7935,7938,7941,7943,7945,7949,7954,7961,7962,7963,7984,8009,8012,8039,8100,8203,8346,8416,8470,8490,8528,8601,8634,8671,8674,8677,8679,8682,8683,8688,8694,8717,8742,8748,8764,8862,8961,9169,9223,9243,9281,9354,9385,9418,9421,9424,9427,9428,9432,9437,9444,9446,9468,9493,9518,9579,9682,9820,9825,9894,9968,10006,10079,10112,10149,10152,10155,10157,10160,10161,10166,10173,10196,10222,10305,10404,10543,10613,10667,10687,10725,10798,10826,10830,10863,10866,10869,10871,10873,10877,10882,10889,10890,10891,10912,10937,10940,10967,11028,11131,11274,11344,11398,11418,11456,11529,11562,11599,11602,11605,11607,11610,11611,11616,11622,11645,11670,11676,11692 dcaps: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ncap,ccap dncap: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ncap COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dccap: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ccap COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances
dbb: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,bb COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dasp: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,asp COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dser: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ser COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dala: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ala COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances darg: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,arg COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dgly: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,gly COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dphe: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,phe COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dlys: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,lys COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dlys2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,lys2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dpro: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,pro COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dgly2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,gly2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dlys3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,lys3 COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances darg2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,arg2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dcaps ATthe positions of the wall=0.8 KAPPAthe force constant for the wall=100000 LABELa label for the action so that its output can be referenced in the input to other actions=dcaps_min UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dcaps ATthe positions of the wall=1.8 KAPPAthe force constant for the wall=100000 LABELa label for the action so that its output can be referenced in the input to other actions=dcaps_max LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dncap.z ATthe positions of the wall=0.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=dncap_min LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dccap.z ATthe positions of the wall=0.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=dccap_min
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dbb.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dbb UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dasp.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dasp UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dser.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dser UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dala.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dala UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=darg.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_darg UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dgly.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dgly UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dphe.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dphe UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dlys.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dlys UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dlys2.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dlys2 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dpro.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dpro UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dgly2.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dgly2 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dlys3.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dlys3 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=darg2.z ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_darg2
GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=11713-11919 LABELa label for the action so that its output can be referenced in the input to other actions=rg
PBMETADUsed to performed Parallel Bias metadynamics. More details ... WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR ARGthe labels of the scalars on which the bias will act=dbb.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 SIGMAthe widths of the Gaussian hills=0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02 HEIGHTthe height of the Gaussian hills, one for all biases=1.2 #kJ/mol PACEthe frequency for hill addition, one for all biases=1000 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=20 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298.0 LABELa label for the action so that its output can be referenced in the input to other actions=PBMETAD GRID_MINthe lower bounds for the grid=-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0,0.0 GRID_MAXthe upper bounds for the grid=9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,9.0,8 FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=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 ... PBMETAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dcaps,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.bias STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR