PLUMED-NEST

Project ID: plumID:19.077
Source: ARG_NH.dat
Originally used with PLUMED version: 2.4
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

#RESTART
#CVs 
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=arg.pdb
The MOLINFO action with label  calculates somethingc1The COM action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
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=1-36 #COM from peptide to surface 
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1.x
scalar
the x-component of the vector connecting the two atoms
d1.y
scalar
the y-component of the vector connecting the two atoms
d1.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2332,c1 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 #dist peptide to surface

#restraint 
wall1The UPPER_WALLS action with label wall1 calculates the following quantities:
 Quantity   
 Type   
 Description  
wall1.bias
scalar
the instantaneous value of the bias potential
wall1.force2
scalar
the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.z ATthe positions of the wall=3.0 KAPPAthe force constant for the wall=1500

#pb
METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=d1.z
SIGMAthe widths of the Gaussian hills=0.05
HEIGHTthe heights of the Gaussian hills=0.2 #kj/mol
PACEthe frequency for hill addition=500 
BIASFACTORuse well tempered metadynamics and use this bias factor=10
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
GRID_MINthe lower bounds for the grid=0.0
GRID_MAXthe upper bounds for the grid=7.0
LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
FILE a file in which the list of added hills is stored=HILLS.d1
... METAD


PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1.z,metad.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