PLUMED-NEST

Project ID: plumID:25.029
Source: ./amor/3-production_mtd_hrex_amor.dat
Originally used with PLUMED version: 2.8
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

#SETTINGS NREPLICAS=2
## production run md: mtd + hrex aPET-PETase
#
#RESTART

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=1-3922      #3832 ENTITY1=3833-3922 # prot0 lig1

The WHOLEMOLECULES action with label  calculates somethingDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=d0    ATOMSthe pair of atom that we are calculating the distance between=1911,3857                       # cat 160 SER OG vs UNK C19
The DISTANCE action with label d0 calculates the following quantities:
 Quantity   
 Description  
d0.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=d1    ATOMSthe pair of atom that we are calculating the distance between=3853,3885                         # ext UNK C17 vs C39
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=h0    ATOMSthe pair of atom that we are calculating the distance between=1915,3858                         # oxh 161 MET N vs O7
The DISTANCE action with label h0 calculates the following quantities:
 Quantity   
 Description  
h0.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=h1    ATOMSthe pair of atom that we are calculating the distance between=797,3858                         # oxh 87 TYR N vs O7
The DISTANCE action with label h1 calculates the following quantities:
 Quantity   
 Description  
h1.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=s0    ATOMSthe pair of atom that we are calculating the distance between=1911,2991                    # cat 237 HIS NE2 vs cat 160 SER OG
The DISTANCE action with label s0 calculates the following quantities:
 Quantity   
 Description  
s0.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=x0    ATOMSthe pair of atom that we are calculating the distance between=1911,1915                      # cat 160 SER OG vs oxh 161 MET N     # autohinibition
The DISTANCE action with label x0 calculates the following quantities:
 Quantity   
 Description  
x0.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=x1    ATOMSthe pair of atom that we are calculating the distance between=1911,797                      # cat 160 SER OG vs oxh 87 TYR N     # autohinibition

The DISTANCE action with label x1 calculates the following quantities:
 Quantity   
 Description  
x1.value
the DISTANCE between this pair of atomsmetad: METADUsed to performed metadynamics on one or more collective variables. More details ...

    ARGthe labels of the scalars on which the bias will act=h0,h1                         # h0,h1
    SIGMAthe widths of the Gaussian hills=0.05,0.05                 # 0.5*fluctuation ~ 1A
    HEIGHTthe heights of the Gaussian hills=@replicas:This keyword specifies that different replicas have different values for this quantity.  See here for more details.0.5,0.564646,0.637648,0.720091,0.813191,0.918329,1.03706,1.17114                               # standard ~0.1-1.0*kBT KJ/mol | ~0.02-1.20 d, ~1.0-2.0 a -> TAU???
    PACEthe frequency for hill addition=500                        # ~100-500 steps relax system before next hill add # change from 400 to 500!!!
    BIASFACTORuse well tempered metadynamics and use this bias factor=15                   # barriers 20-30 KJ/mol need a bias factor of ~10-15 biol syst # change from 30 to 15!!!
    TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298                      # well-tempered
    GRID_MINthe lower bounds for the grid=-1.0,-1.0
    GRID_MAXthe upper bounds for the grid=2.0,2.0                # max min values cv, store hills in file, memory efficient ?

...

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=h0 ATthe positions of the wall=0.6 KAPPAthe force constant for the wall=5000 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=h0_uwall        # 6A max distance from hole
The UPPER_WALLS action with label h0_uwall calculates the following quantities:
 Quantity   
 Description  
h0_uwall.bias
the instantaneous value of the bias potential
h0_uwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=h1 ATthe positions of the wall=0.6 KAPPAthe force constant for the wall=5000 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=h1_uwall        # 6A max distance from hole
#UPPER_WALLS ARG=s0 AT=0.6 KAPPA=5000 EXP=2 EPS=1 OFFSET=0 LABEL=s0_uwall        # 6A max distance from hole
#UPPER_WALLS ARG=d0 AT=0.6 KAPPA=5000 EXP=2 EPS=1 OFFSET=0 LABEL=d0_uwall        # 6A max distance from ser
#LOWER_WALLS ARG=x0 AT=0.6 KAPPA=5000 EXP=2 EPS=1 OFFSET=0 LABEL=x0_uwall        # 6A max distance from hole
#LOWER_WALLS ARG=x1 AT=0.6 KAPPA=5000 EXP=2 EPS=1 OFFSET=0 LABEL=x1_uwall        # 6A max distance from hole

The UPPER_WALLS action with label h1_uwall calculates the following quantities:
 Quantity   
 Description  
h1_uwall.bias
the instantaneous value of the bias potential
h1_uwall.force2
the instantaneous value of the squared force due to this bias potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=2.4 KAPPAthe force constant for the wall=2550 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=d1_lwall        # amorphous stretch

The LOWER_WALLS action with label d1_lwall calculates the following quantities:
 Quantity   
 Description  
d1_lwall.bias
the instantaneous value of the bias potential
d1_lwall.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint 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=1000 FILEthe name of the file on which to output these quantities=colvar #print less