PLUMED-NEST

Project ID: plumID:24.028
Source: inputs/tip3p/GU/metadyn/plumed_metad.dat
Originally used with PLUMED version: 2.9
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

# Activate MOLINFO functionalities
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=../conf.pdb

The MOLINFO action with label  calculates somethingrnaThe GROUP action with label rna calculates the following quantities:
 Quantity   
 Type   
 Description  
rna
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=../indices.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=RNA
rnacenterThe CENTER_FAST action with label rnacenter calculates the following quantities:
 Quantity   
 Type   
 Description  
rnacenter
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=rna
posrnaThe POSITION action with label posrna calculates the following quantities:
 Quantity   
 Type   
 Description  
posrna.x
scalar
the x-component of the atom position
posrna.y
scalar
the y-component of the atom position
posrna.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=rnacenter
membThe GROUP action with label memb calculates the following quantities:
 Quantity   
 Type   
 Description  
memb
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=../indices.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=C116
membcenterThe CENTER_FAST action with label membcenter calculates the following quantities:
 Quantity   
 Type   
 Description  
membcenter
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=memb
posmembThe POSITION action with label posmemb calculates the following quantities:
 Quantity   
 Type   
 Description  
posmemb.x
scalar
the x-component of the atom position
posmemb.y
scalar
the y-component of the atom position
posmemb.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=membcenter
dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d.a
scalar
the normalized projection on the first lattice vector of the vector connecting the two atoms
d.b
scalar
the normalized projection on the second lattice vector of the vector connecting the two atoms
d.c
scalar
the normalized projection on the third lattice vector 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=rnacenter,membcenter SCALED_COMPONENTS calculate the a, b and c scaled components of the distance separately and store them as label
scaled_zdistThe COMBINE action with label scaled_zdist calculates the following quantities:
 Quantity   
 Type   
 Description  
scaled_zdist
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d.c COEFFICIENTS the coefficients of the arguments in your function=7.636 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-3.818,3.818
metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.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=scaled_zdist SIGMAthe widths of the Gaussian hills=0.02 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=5 PACEthe frequency for hill addition=200 BIASFACTORuse well tempered metadynamics and use this bias factor=5 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=323
   GRID_MINthe lower bounds for the grid=-3.818 GRID_MAXthe upper bounds for the grid=3.818
...
metad: 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=scaled_zdist SIGMAthe widths of the Gaussian hills=0.02 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=5 PACEthe frequency for hill addition=200 BIASFACTORuse well tempered metadynamics and use this bias factor=5 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=323
   GRID_MINthe lower bounds for the grid=-3.818 GRID_MAXthe upper bounds for the grid=3.818
 FILE a file in which the list of added hills is stored=HILLS
...


PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=scaled_zdist,metad.bias FILEthe name of the file on which to output these quantities=METADYN STRIDE the frequency with which the quantities of interest should be output=5000