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 details ATOMSthe list of atoms which are involved the virtual atom's definition=11717,11718,11719,11728,11731,11732,11733,11742,11745,11746,11747,11764,11767,11768,11769,11786,11789,11790,11791,11800,11803,11804,11805,11813,11816,11817,11818,11827,11830,11831,11832,11851,11854,11855,11856,11865,11868,11869,11870,11878,11881,11882,11883,11892,11895,11896,11897,11914,11917,11918,11919,11927,11930,11931,11932,11941,11944,11945,11946,11963,11966,11967,11968,11984,11987,11988,11989,12005,12008,12009,12010,12024,12027,12028,12029,12043,12046,12047,12048 # Head Groups: CB + on head: 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 ser1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11720-11727 ser2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11734-11741 lys1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11748-11763 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=11770-11785 ser3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11792-11799 gly1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11806-11812 ser4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11819-11826 tyr1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11833-11850 ser5: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11857-11864 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=11871-11877 ser6: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11884-11891 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=11898-11913 gly3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11920-11926 ser7: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11933-11940 lys4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11947-11962 arg1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11969-11983 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=11990-12004 ile1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=12011-12023 leu1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=12030-12042 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 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 dhead: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,head 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 dser1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ser1 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 dser2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ser2 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 dlys1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,lys1 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 dser3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ser3 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 dgly1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,gly1 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 dser4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ser4 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 dtyr1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,tyr1 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 dser5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ser5 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 dser6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ser6 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 dgly3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,gly3 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 dser7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ser7 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 dlys4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,lys4 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 darg1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,arg1 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 dile1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ile1 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 dleu1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,leu1 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
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=6.0 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=dhead.z ATthe positions of the wall=6.0 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_dhead UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dser1.z ATthe positions of the wall=6.0 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_dser1 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dser2.z ATthe positions of the wall=6.0 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_dser2 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dlys1.z ATthe positions of the wall=6.0 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_dlys1 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=6.0 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=dser3.z ATthe positions of the wall=6.0 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_dser3 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dgly1.z ATthe positions of the wall=6.0 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_dgly1 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dser4.z ATthe positions of the wall=6.0 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_dser4 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dtyr1.z ATthe positions of the wall=6.0 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_dtyr1 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dser5.z ATthe positions of the wall=6.0 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_dser5 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=6.0 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=dser6.z ATthe positions of the wall=6.0 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_dser6 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=6.0 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=dgly3.z ATthe positions of the wall=6.0 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_dgly3 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dser7.z ATthe positions of the wall=6.0 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_dser7 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dlys4.z ATthe positions of the wall=6.0 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_dlys4 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=darg1.z ATthe positions of the wall=6.0 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_darg1 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=6.0 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 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dile1.z ATthe positions of the wall=6.0 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_dile1 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dleu1.z ATthe positions of the wall=6.0 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_dleu1
# Radius of Gyration: All atoms in chain 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=11713-12050 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,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,rg SIGMAthe widths of the Gaussian hills=200.0 ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01 SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4 HEIGHTthe height of the Gaussian hills, one for all biases=1.2 #kJ/mol PACEthe frequency for hill addition, one for all biases=500 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=35 # Sqrt[cv]*8 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 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=-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,-0.5,0.0 GRID_MAXthe upper bounds for the grid=6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.5,6.0 FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=../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 ... PBMETAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=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,rg 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