PLUMED-NEST

Project ID: plumID:23.014
Source: CXCR4_dimer/plumed_CXCR4_dimer.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 STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=62,131,132,220,222,226,230,232,324,418,517,521,526,622,634 ENTITY1the atoms that make up a molecule that you wish to align=718,787,788,876,878,882,886,888,980,1074,1173,1177,1182,1278,1290

The WHOLEMOLECULES action with label  calculates somethingcomAThe COM action with label comA calculates the following quantities:
 Quantity   
 Type   
 Description  
comA
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=554,558
comBThe COM action with label comB calculates the following quantities:
 Quantity   
 Type   
 Description  
comB
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=21,162,181,345,400,552,603
comCThe COM action with label comC calculates the following quantities:
 Quantity   
 Type   
 Description  
comC
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=733,775,898,958,1102,1166,1300
comDThe COM action with label comD calculates the following quantities:
 Quantity   
 Type   
 Description  
comD
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=955,958
com1The COM action with label com1 calculates the following quantities:
 Quantity   
 Type   
 Description  
com1
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=62,131,132,220,222,226,230,232,324,418,517,521,526,622,634
com2The COM action with label com2 calculates the following quantities:
 Quantity   
 Type   
 Description  
com2
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=718,787,788,876,878,882,886,888,980,1074,1173,1177,1182,1278,1290
dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d.x
scalar
the x-component of the vector connecting the two atoms
d.y
scalar
the y-component of the vector connecting the two atoms
d.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=com1,com2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
ddThe COMBINE action with label dd calculates the following quantities:
 Quantity   
 Type   
 Description  
dd
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d.x,d.y POWERS the powers to which you are raising each of the arguments in your function=2,2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d2The COMBINE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=dd POWERS the powers to which you are raising each of the arguments in your function=0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
torsionThe TORSION action with label torsion calculates the following quantities:
 Quantity   
 Type   
 Description  
torsion
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=comA,comB,comC,comD

mThe METAD action with label m calculates the following quantities:
 Quantity   
 Type   
 Description  
m.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=d2,torsion SIGMAthe widths of the Gaussian hills=0.04,0.06 HEIGHTthe heights of the Gaussian hills=0.5 PACEthe frequency for hill addition=5000 BIASFACTORuse well tempered metadynamics and use this bias factor=20 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 GRID_MINthe lower bounds for the grid=1.3,-pi GRID_MAXthe upper bounds for the grid=8.5,pi GRID_WFILEthe file on which to write the grid=GRID_W.dat GRID_WSTRIDEwrite the grid to a file every N steps=1000000 WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
m: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=d2,torsion SIGMAthe widths of the Gaussian hills=0.04,0.06 HEIGHTthe heights of the Gaussian hills=0.5 PACEthe frequency for hill addition=5000 BIASFACTORuse well tempered metadynamics and use this bias factor=20 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 GRID_MINthe lower bounds for the grid=1.3,-pi GRID_MAXthe upper bounds for the grid=8.5,pi GRID_WFILEthe file on which to write the grid=GRID_W.dat GRID_WSTRIDEwrite the grid to a file every N steps=1000000 WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR  FILE a file in which the list of added hills is stored=HILLS

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d2 ATthe positions of the wall=8.0 KAPPAthe force constant for the wall=5000000.0 EXP the powers for the walls=2.0 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=uwalliThe UPPER_WALLS action with label uwalli calculates the following quantities:
 Quantity   
 Type   
 Description  
uwalli.bias
scalar
the instantaneous value of the bias potential
uwalli.force2
scalar
the instantaneous value of the squared force due to this bias potential

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d2,torsion STRIDE the frequency with which the quantities of interest should be output=5000 FILEthe name of the file on which to output these quantities=COLVAR
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1000000