PLUMED-NEST

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

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


The WHOLEMOLECULES action with label  calculates somethingligThe COM action with label lig calculates the following quantities:
 Quantity   
 Type   
 Description  
lig
atoms
virtual atom calculated by COM action: 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


d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,1533
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,1716
d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2285
d4The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
d4
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2005
d5The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Type   
 Description  
d5
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,1905
d6The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Type   
 Description  
d6
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2239 
d7The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Type   
 Description  
d7
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2424
d8The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Type   
 Description  
d8
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=lig,2523

helix1The COM action with label helix1 calculates the following quantities:
 Quantity   
 Type   
 Description  
helix1
atoms
virtual atom calculated by COM action: 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
helix2The COM action with label helix2 calculates the following quantities:
 Quantity   
 Type   
 Description  
helix2
atoms
virtual atom calculated by COM action: 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
helix3The COM action with label helix3 calculates the following quantities:
 Quantity   
 Type   
 Description  
helix3
atoms
virtual atom calculated by COM action: 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
helix4The COM action with label helix4 calculates the following quantities:
 Quantity   
 Type   
 Description  
helix4
atoms
virtual atom calculated by COM action: 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

hd12The DISTANCE action with label hd12 calculates the following quantities:
 Quantity   
 Type   
 Description  
hd12
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix1,helix2
hd23The DISTANCE action with label hd23 calculates the following quantities:
 Quantity   
 Type   
 Description  
hd23
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=helix2,helix3
hd34The DISTANCE action with label hd34 calculates the following quantities:
 Quantity   
 Type   
 Description  
hd34
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs 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=rc1The COMBINE action with label rc1 calculates the following quantities:
 Quantity   
 Type   
 Description  
rc1
scalar
a linear compbination 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=rc2The COMBINE action with label rc2 calculates the following quantities:
 Quantity   
 Type   
 Description  
rc2
scalar
a linear compbination 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=external1The EXTERNAL action with label external1 calculates the following quantities:
 Quantity   
 Type   
 Description  
external1.bias
scalar
the instantaneous value of the bias potential
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action uses the defaults shown here. 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  SCALE a factor that multiplies the external potential, useful to invert free energies=1.0

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=external2The EXTERNAL action with label external2 calculates the following quantities:
 Quantity   
 Type   
 Description  
external2.bias
scalar
the instantaneous value of the bias potential
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action uses the defaults shown here. 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  SCALE a factor that multiplies the external potential, useful to invert free energies=1.0


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