PLUMED-NEST

Project ID: plumID:25.028
Source: C80/plumed1.dat
Originally used with PLUMED version: 2.7
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

#MOLINFO STRUCTURE=npt.gro
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=1-242
The WHOLEMOLECULES action with label  calculates somethingc1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1-242

The CENTER action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
the position of the center of massWATER_OXYGENS: 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 ATOMSthe numerical indexes for the set of atoms in the group=243-66497:3

#COORD: COORDINATION GROUPA=MOL GROUPB=WATER_OXYGENS SWITCH={RATIONAL D_0=0.0 R_0=0.58 NN=50 MM=100} 
#COORD: COORDINATION GROUPA=WATER_OXYGENS GROUPB=MOL R_0=0.59
The GROUP action with label WATER_OXYGENS calculates somethingCOORD: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=c1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WATER_OXYGENS SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.60 NN=5 MM=12}

#compute distance between CA atoms of residues 1 and 40
The COORDINATION action with label COORD calculates the following quantities:
 Quantity   
 Description  
COORD.value
the value of the coordinationr: GYRATIONCalculate the radius of gyration, or other properties related to it. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1-242

#compute distance between CA atoms of residues 1 and 40
The GYRATION action with label r calculates the following quantities:
 Quantity   
 Description  
r.value
the radius that was computed from the weightsd: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,239

# Apply different weights by scaling the collective variables
The DISTANCE action with label d calculates the following quantities:
 Quantity   
 Description  
d.value
the DISTANCE between this pair of atomsSCALED_COORD: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=COORD FUNCthe function you wish to evaluate=(x-5.5)/(40.0-5.5) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label SCALED_COORD calculates the following quantities:
 Quantity   
 Description  
SCALED_COORD.value
an arbitrary functionSCALED_RG: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=r FUNCthe function you wish to evaluate=(x-0.6)/(2.35-0.60) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label SCALED_RG calculates the following quantities:
 Quantity   
 Description  
SCALED_RG.value
an arbitrary functionSCALED_d: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=d FUNCthe function you wish to evaluate=(x-0.40)/(5.4-0.42)  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The MATHEVAL action with label SCALED_d calculates the following quantities:
 Quantity   
 Description  
SCALED_d.value
an arbitrary functionCOMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=lt0 ARGthe values input to this function=SCALED_COORD,SCALED_RG,SCALED_d COEFFICIENTS the coefficients of the arguments in your function=2.16,1.14,-0.28 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

#lt1_1: MATHEVAL ARG=lt1_1 FUNC=x- PERIODIC=NO
The COMBINE action with label lt0 calculates the following quantities:
 Quantity   
 Description  
lt0.value
a linear combinationuwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=lt0 ATthe positions of the wall=3.7 KAPPAthe force constant for the wall=20000 EXP the powers for the walls=4 EPS the values for s_i in the expression for a wall=1.0
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentiallwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=lt0 ATthe positions of the wall=-0.1 KAPPAthe force constant for the wall=20000 EXP the powers for the walls=4 EPS the values for s_i in the expression for a wall=1.0

# Metadynamics bias potential along the first TICA component
# Metadynamics bias potential using TICA and hydration shell count as collective variables
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialmetad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=lt0 SIGMAthe widths of the Gaussian hills=0.35, HEIGHTthe heights of the Gaussian hills=2.0 PACEthe frequency for hill addition=500 BIASFACTORuse well tempered metadynamics and use this bias factor=30.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 GRID_MINthe lower bounds for the grid=-0.5, GRID_MAXthe upper bounds for the grid=4.2

# Print out collective variables for monitoring
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=lt0,COORD,r,d,metad.* FILEthe name of the file on which to output these quantities=colvar1.dat STRIDE the frequency with which the quantities of interest should be output=1000