Project ID: plumID:19.028
Source: Lysozyme/round9/plumed.9.2rc.dat
Originally used with PLUMED version: 2.3
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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WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-2881 lig: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2870,2872,2874 d1: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,1533 d2: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,1716 d3: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2285 d4: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2005 d5: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,1905 d6: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2239 d7: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2424 d8: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2523 helix1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1416,1428,1452,1475,1501,1513,1533,1554,1566 helix2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1964,1980,1994,2005,2028,2052,2071,2094,2111 helix3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2176,2200,2212,2227,2239,2251,2271,2285,2308 helix4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2535,2559,2583,2603,2626,2642,2658,2678,2702 hd12: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix1,helix2 hd23: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix2,helix3 hd34: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix3,helix4 COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=rc1 ARGthe values input to this function=d1,d2,d3,d4,d5,d6,d7,d8,hd12,hd23,hd34 POWERS the powers to which you are raising each of the arguments in your function=1,1,1,1,1,1,1,1,1,1,1 COEFFICIENTS the coefficients of the arguments in your function=0.4930809380065504,0.5058593109729893,-0.4001714129673795,0.23349420293166986,0.030037136299780397,-0.40087790689897096,0.1229390189050703,0.23125338096805748,-0.20809724216770412,-0.11136820637118663,-0.02039729281248875 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=rc2 ARGthe values input to this function=d1,d2,d3,d4,d5,d6,d7,d8,hd12,hd23,hd34 POWERS the powers to which you are raising each of the arguments in your function=1,1,1,1,1,1,1,1,1,1,1 COEFFICIENTS the coefficients of the arguments in your function=0.47798774048355186,0.5938376978731852,-0.3911931737431559,-0.25477549844776715,-0.1867757539217771,-0.3460145457220869,0.01717439149939613,0.07070895480558717,-0.059124920936706925,-0.13513219665156984,-0.1388503646899041 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=rc1 FILEthe name of the file containing the external potential=static_bias.8.txt LABELa label for the action so that its output can be referenced in the input to other actions=external1
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=rc2 FILEthe name of the file containing the external potential=static_bias.9.rc2.txt LABELa label for the action so that its output can be referenced in the input to other actions=external2
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,d3,d4,d5,d6,d7,d8,hd12,hd23,hd34,rc1,rc2,external1.bias,external2.bias STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=benzene_Lyso_T298_9