PLUMED-NEST

Project ID: plumID:23.016
Source: plumed.dat
Originally used with PLUMED version: 2.5.3
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

#RESTART
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=adr_bin_ref.pdb
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis 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=1-4903

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 between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=489,4651
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 between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=887,1501
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 between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1570,2021
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 between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3257,3710
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 between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4112,4322

MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=AindexThe MATHEVAL action with label Aindex calculates the following quantities:
 Quantity   
 Type   
 Description  
Aindex
scalar
an arbitrary function
  ARGthe values input to this function=d1,d2,d3,d4,d5
  VARthe names to give each of the arguments in the function=x,y,z,a,b
  FUNCthe function you wish to evaluate=((-14.43*x-7.62*y+9.11*z-6.32*a-5.22*b)+27.888)
  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

tm3-tm6_1The DISTANCE action with label tm3-tm6_1 calculates the following quantities:
 Quantity   
 Type   
 Description  
tm3-tm6_1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1687,3710
tm3-tm6_2The DISTANCE action with label tm3-tm6_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
tm3-tm6_2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1687,3646
yyThe DISTANCE action with label yy calculates the following quantities:
 Quantity   
 Type   
 Description  
yy
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3133,4629 
NPxxY_iThe RMSD action with label NPxxY_i calculates the following quantities:
 Quantity   
 Type   
 Description  
NPxxY_i
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=NPxxY_inact_backbone_adr.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL 
NPxxY_i: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=NPxxY_inact_backbone_adr.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
PIF_iThe RMSD action with label PIF_i calculates the following quantities:
 Quantity   
 Type   
 Description  
PIF_i
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PIF_inact_adr.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
PIF_i: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=PIF_inact_adr.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
tm5The DISTANCE action with label tm5 calculates the following quantities:
 Quantity   
 Type   
 Description  
tm5
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2926,4461

metaThe METAD action with label meta calculates the following quantities:
 Quantity   
 Type   
 Description  
meta.bias
scalar
the instantaneous value of the bias potential
meta.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
meta.rct
scalar
the reweighting factor c(t).: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=Aindex SIGMAthe widths of the Gaussian hills=0.1 HEIGHTthe heights of the Gaussian hills=1 PACEthe frequency for hill addition=500 FILE a file in which the list of added hills is stored=../HILLS BIASFACTORuse well tempered metadynamics and use this bias factor=5. GRID_MINthe lower bounds for the grid=-50 GRID_MAXthe upper bounds for the grid=50 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* 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