Project ID: plumID:23.037
Source: SBP_plumed_nest/Plumed_files/K8AK11A/plumed.dat
Originally used with PLUMED version: 2.6
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=K8AK11A_ACE_NME.pdb # com: COM ATOMS=9025-9207 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=9025-9030 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=9202-9207 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=9029,9030,9031,9033,9041,9042,9043,9045,9052,9053,9054,9056,9062,9063,9064,9066,9086,9087,9088,9090,9093,9094,9095,9097,9113,9114,9115,9117,9135,9136,9137,9139,9145,9146,9147,9151,9159,9160,9161,9163,9166,9167,9168,9170,9176,9177,9178,9180,9200,9201,9202,9204 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=9035-9040 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=9047-9051 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=9058-9061 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=9068-9085 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=9090-9092 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=9099-9112 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=9119-9134 ala2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=9141-9144 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=9153-9158 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=9163-9165 ala3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=9172-9175 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=9182-9199 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=38,49,52,54,56,59,62,65,67,69,72,74,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,2294,2305,2308,2310,2312,2315,2318,2321,2323,2325,2328,2330,2392,2393,2394,2395,2396,2397,2398,2399,2400,2401,2402,2403,2404,2405,2406,2407,2408,2409,2410,2411,2412,2413,2414,2415,2416,2417,2418,2419,2420,2421,2422,2423,2424,2425,2426,2427,2428,2429,2430,2431,2432,2433,2434,2435,2436,2437,2438,2439,2440,2441,2442,2443,2444,2445,2446,2447,4550,4561,4564,4566,4568,4571,4574,4577,4579,4581,4584,4586,4648,4649,4650,4651,4652,4653,4654,4655,4656,4657,4658,4659,4660,4661,4662,4663,4664,4665,4666,4667,4668,4669,4670,4671,4672,4673,4674,4675,4676,4677,4678,4679,4680,4681,4682,4683,4684,4685,4686,4687,4688,4689,4690,4691,4692,4693,4694,4695,4696,4697,4698,4699,4700,4701,4702,4703,6806,6817,6820,6822,6824,6827,6830,6833,6835,6837,6840,6842,6904,6905,6906,6907,6908,6909,6910,6911,6912,6913,6914,6915,6916,6917,6918,6919,6920,6921,6922,6923,6924,6925,6926,6927,6928,6929,6930,6931,6932,6933,6934,6935,6936,6937,6938,6939,6940,6941,6942,6943,6944,6945,6946,6947,6948,6949,6950,6951,6952,6953,6954,6955,6956,6957,6958,6959 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 # dcom: DISTANCE ATOMS=top_oh,com COMPONENTS NOPBC
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 dala2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ala2 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 dala3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=top_oh,ala3 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
# UPPER_WALLS ARG=dcom.z AT=5.5 KAPPA=1000000 LABEL=uwall_dcom 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=1.2 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=0.7 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=0.7 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=dala2.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_dala2 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=dala3.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_dala3 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=9025-9207 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,dala2.z,dpro.z,dgly2.z,dala3.z,darg2.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 SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=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 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=30 # Sqrt[cv]*8 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=-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=7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0 FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=../HILLS.dbb,../HILLS.dasp,../HILLS.dser,../HILLS.dala,../HILLS.darg,../HILLS.dgly,../HILLS.dphe,../HILLS.dlys,../HILLS.dala2,../HILLS.dpro,../HILLS.dgly2,../HILLS.dala3,../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=PBMETAD.bias,dcaps,dbb.z,dncap.z,dccap.z,dasp.z,dser.z,dala.z,darg.z,dgly.z,dphe.z,dlys.z,dala2.z,dpro.z,dgly2.z,dala3.z,darg2.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