Project ID: plumID:21.042
Source: Plumed_nest/plumed_Nce6Ncp6_Au111.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=Nce6Ncp6.pdb ## ENERGY LABEL=energy
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=7201,7203,7206,7225,7226,7229,7248,7249,7252,7271,7272,7275,7294,7295,7298,7317,7318,7321,7340,7341,7344,7355,7356,7359,7370,7371,7374,7385,7386,7389,7400,7401,7404,7415,7416,7419 pr1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7211,7214-7224 pr2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7234,7237-7247 pr3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7257,7260-7270 pr4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7280,7283-7293 pr5: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7303,7306-7316 pr6: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7326,7329-7339 cc1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7346-7354 cc2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7361-7369 cc3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7376-7384 cc4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7391-7399 cc5: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7406-7414 cc6: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=7421-7429 ## com: COM ATOMS=7201-7432
dbb: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,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 dpr1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,pr1 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 dpr2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,pr2 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 dpr3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,pr3 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 dpr4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,pr4 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 dpr5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,pr5 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 dpr6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,pr6 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 dcc1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,cc1 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 dcc2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,cc2 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 dcc3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,cc3 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 dcc4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,cc4 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 dcc5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,cc5 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 dcc6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7200,cc6 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=7200,com COMPONENTS NOPBC
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=8.0 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=dpr1.z ATthe positions of the wall=8.0 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_dpr1 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dpr2.z ATthe positions of the wall=8.0 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_dpr2 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dpr3.z ATthe positions of the wall=8.0 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_dpr3 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dpr4.z ATthe positions of the wall=8.0 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_dpr4 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dpr5.z ATthe positions of the wall=8.0 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_dpr5 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dpr6.z ATthe positions of the wall=8.0 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_dpr6 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dcc1.z ATthe positions of the wall=8.0 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_dcc1 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dcc2.z ATthe positions of the wall=8.0 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_dcc2 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dcc3.z ATthe positions of the wall=8.0 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_dcc3 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dcc4.z ATthe positions of the wall=8.0 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_dcc4 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dcc5.z ATthe positions of the wall=8.0 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_dcc5 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dcc6.z ATthe positions of the wall=8.0 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_dcc6
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=7201-7432 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,dpr1.z,dpr2.z,dpr3.z,dpr4.z,dpr5.z,dpr6.z,dcc1.z,dcc2.z,dcc3.z,dcc4.z,dcc5.z,dcc6.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=500 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=0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0 GRID_MAXthe upper bounds for the grid=8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,8.0,7 FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS.dbb,HILLS.dpr1,HILLS.dpr2,HILLS.dpr3,HILLS.dpr4,HILLS.dpr5,HILLS.dpr6,HILLS.dcc1,HILLS.dcc2,HILLS.dcc3,HILLS.dcc4,HILLS.dcc5,HILLS.dcc6,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,dpr1.z,dpr2.z,dpr3.z,dpr4.z,dpr5.z,dpr6.z,dcc1.z,dcc2.z,dcc3.z,dcc4.z,dcc5.z,dcc6.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