Project ID: plumID:19.028
Source: Lysozyme/round10/plumed.10.2rc.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
tested onv2.10
tested onmaster
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=0.4013018506074015,0.5347381495345983,-0.4293710203075956,-0.23981491902544105,-0.24741461591361635,-0.3881314288406267,0.0053029323724150335,0.09556606133639899,0.09356899271449744,-0.11085507070054638,-0.2628236541370427 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.10.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_10