Project ID: plumID:22.026
Source: Silica_peptoid_PB/nae/plumed.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
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=AhxNae6.pdb 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=2947,2948,2949,2950,2953,2954,2965,2966,2969,2970,2981,2982,2985,2986,2997,2998,3001,3002,3013,3014,3017,3018,3029,3030,3033,3034 U1 : COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2929-2946 U2 : COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2955-2964 U3 : COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2971-2980 U4 : COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2987-2996 U5 : COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3003-3012 U6 : COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3019-3028 U7 : COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3035-3047 surf : 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 dbb : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,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 dU1 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,U1 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 dU2 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,U2 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 dU3 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,U3 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 dU4 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,U4 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 dU5 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,U5 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 dU6 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,U6 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 dU7 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,U7 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=4.5 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_bb UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dU1.z ATthe positions of the wall=4.5 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_U1 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dU2.z ATthe positions of the wall=4.5 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_U2 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dU3.z ATthe positions of the wall=4.5 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_U3 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dU4.z ATthe positions of the wall=4.5 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_U4 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dU5.z ATthe positions of the wall=4.5 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_U5 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dU6.z ATthe positions of the wall=4.5 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_U6 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dU7.z ATthe positions of the wall=4.5 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_U7
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=2929-3047 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,dU1.z,dU2.z,dU3.z,dU4.z,dU5.z,dU6.z,dU7.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 SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.5 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=25 # 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,-0.5,0.0 GRID_MAXthe upper bounds for the grid=5.5,5.5,5.5,5.5,5.5,5.5,5.5,5.5,4.0 FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=../HILLS.dbb,../HILLS.dU1,../HILLS.dU2,../HILLS.dU3,../HILLS.dU4,../HILLS.dU5,../HILLS.dU6,../HILLS.dU7,../HILLS.rg ... PBMETAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dbb.z,dU1.z,dU2.z,dU3.z,dU4.z,dU5.z,dU6.z,dU7.z,rg,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