PLUMED-NEST-TEST-SITE

Project ID: plumID:25.010
Source: input_plumed/plumed_mego.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

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=1-1629 ENTITY1the atoms that make up a molecule that you wish to align=1630-1638

# Group definition
The WHOLEMOLECULES action with label  calculates somethingpockThe GROUP action with label pock calculates the following quantities:
 Quantity   
 Type   
 Description  
pock
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)=../index_files/index_mego.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Pocket
benThe GROUP action with label ben calculates the following quantities:
 Quantity   
 Type   
 Description  
ben
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)=../index_files/index_mego.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=BEN

pock_centerThe COM action with label pock_center calculates the following quantities:
 Quantity   
 Type   
 Description  
pock_center
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=pock
ben_centerThe COM action with label ben_center calculates the following quantities:
 Quantity   
 Type   
 Description  
ben_center
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=ben

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=pock_center,ben_center

ABMDAdds a ratchet-and-pawl like restraint on one or more variables. More details ...
   LABELa label for the action so that its output can be referenced in the input to other actions=rmdThe ABMD action with label rmd calculates the following quantities:
 Quantity   
 Type   
 Description  
rmd.bias
scalar
the instantaneous value of the bias potential
rmd.d1_min
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file.  These quantities will be named with the arguments of the bias followed by the character string _min. These quantities tell the user the minimum value assumed by rho_m(t). This particular component measures this quantity for the input CV named d1
rmd.force2
scalar
the instantaneous value of the squared force due to this bias potential
   ARGthe labels of the scalars on which the bias will act=d1
   TOThe array of target values=3.5
   KAPPAThe array of force constants=100 
... ABMD


COMMITTORDoes a committor analysis. More details ...
   ARGthe labels of the values which is being used to define the committor surface=d1
   STRIDE the frequency with which the CVs are analyzed=200 
   BASIN_LL1List of lower limits for basin #=3.2
   BASIN_UL1List of upper limits for basin #=3.6 
...

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1 FILEthe name of the file on which to output these quantities=distance.dat STRIDE the frequency with which the quantities of interest should be output=200
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rmd.* FILEthe name of the file on which to output these quantities=rmd_data.dat STRIDE the frequency with which the quantities of interest should be output=200

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=200