Project ID: plumID:21.027
Source: L858R/plumed.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
tested onv2.10
tested onmaster
#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=L858R_active.pdb 
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=1-4722

# Distances describing the two saltbridges K745(NZ):E762(CD) and K745(ΝΖ):D855(CG)
# that reflect the conformation of the aC helix
# (CVs described in Ludo's paper doi:10.1073/pnas.1221953110)

K745_E762: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=745,1078
K745_D855: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=745,2521

# Distance between the two distance
# When both saltbridges are formed, the distance between the two distances (CV)
# is close to 0. This CV is able to characterise the displacement of the fuctionally important
# E762 located in the aC helix of the N-lobe in its transition from the so-called "aC-in" to "aC-out" conformation
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=d
    ARGthe values input to this function=K745_E762,K745_D855
    VARthe names to give each of the arguments in the function=a,b
    FUNCthe function you wish to evaluate=a-b
    PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

# Distance from active cmap
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cmap_active.dat

# Distance form inactive cmap
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cmap_inactive.dat
# Confine the explored space
lwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d ATthe positions of the wall=-1.5 KAPPAthe force constant for the wall=4000.0
uwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cmap_active,cmap_inactive,d ATthe positions of the wall=65,65,2.5 KAPPAthe force constant for the wall=3500.0,3500.0,4000.0

# Gaussians from an initial metaD sim where the energy was biased
# will be loaded to perform the second metaD in the WTE
ene: ENERGYCalculate the total potential energy of the simulation box. More details
METADUsed to performed metadynamics on one or more collective variables. More details ...
    LABELa label for the action so that its output can be referenced in the input to other actions=wte
    ARGthe labels of the scalars on which the bias will act=ene PACEthe frequency for hill addition=1000000 HEIGHTthe heights of the Gaussian hills=2 SIGMAthe widths of the Gaussian hills=1100 # Deposit a Gaussian to the potential energy every 2 ns
    FILE a file in which the list of added hills is stored=HILLS_PTWE 
    BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=@replicas:This keyword specifies that different replicas have different values for this quantity.  See here for more details.300,305,310,318,326,335,344,354,363,375,382
... METAD

# Activate metaD on the rest of the CVs
METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
    LABELa label for the action so that its output can be referenced in the input to other actions=meta
    ARGthe labels of the scalars on which the bias will act=cmap_active,cmap_inactive,d HEIGHTthe heights of the Gaussian hills=3.0 SIGMAthe widths of the Gaussian hills=0.5,0.5,0.15 PACEthe frequency for hill addition=500 
    GRID_MINthe lower bounds for the grid=0,0,-2 GRID_MAXthe upper bounds for the grid=70,70,3 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.25,0.25,0.075 
    BIASFACTORuse well tempered metadynamics and use this bias factor=10 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=@replicas:This keyword specifies that different replicas have different values for this quantity.  See here for more details.300,305,310,318,326,335,344,354,363,375,382
... METAD

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 FMTthe format that should be used to output real numbers=%8.4f