PLUMED-NEST

Project ID: plumID:21.001
Source: HS2ST/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

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#DO NOT LOOK AT Plucker right now, theta and phi can only see one boat conformation
PUCKERING Calculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=14614,14612,14626,14622,14620,14615  LABELa label for the action so that its output can be referenced in the input to other actions=puckThe PUCKERING action with label puck calculates the following quantities:
 Quantity   
 Type   
 Description  
puck.qx
scalar
Cartesian component x (6 membered rings)
puck.qy
scalar
Cartesian component y (6 membered rings)
puck.qz
scalar
Cartesian component z (6 membered rings)
puck.phi
scalar
Pseudorotation phase (6 membered rings)
puck.theta
scalar
Theta angle (6 membered rings)
puck.amplitude
scalar
Pseudorotation amplitude (6 membered rings)

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#set up distance iduo2-papsS
O2The GROUP action with label O2 calculates the following quantities:
 Quantity   
 Type   
 Description  
O2
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 ATOMSthe numerical indexes for the set of atoms in the group=14628
SThe GROUP action with label S calculates the following quantities:
 Quantity   
 Type   
 Description  
S
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 ATOMSthe numerical indexes for the set of atoms in the group=14727
dPThe DISTANCE action with label dP calculates the following quantities:
 Quantity   
 Type   
 Description  
dP
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=O2,S
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metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=dP,puck.qx,puck.qy,puck.qz PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=2.0 SIGMAthe widths of the Gaussian hills=0.1,0.2,0.2,0.2 FILE a file in which the list of added hills is stored=HILLS3 BIASFACTORuse well tempered metadynamics and use this bias factor=50.0 GRID_MINthe lower bounds for the grid=0,-pi,-pi,-pi GRID_MAXthe upper bounds for the grid=1.2,2pi,2pi,2pi TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 GRID_BINthe number of bins for the grid=100,100,100,100

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dP ATthe positions of the wall=1 KAPPAthe force constant for the wall=35100 EXP the powers for the walls=2 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=uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dP,puck.qz ATthe positions of the wall=0.3,0.05 KAPPAthe force constant for the wall=35100,1000.0 EXP the powers for the walls=2,2 OFFSET the offset for the start of the wall=0,0 LABELa label for the action so that its output can be referenced in the input to other actions=lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential


# monitor the two variables and the metadynamics bias potential
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=*  FILEthe name of the file on which to output these quantities=COLVAR

The PRINT action with label  calculates somethingPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=puck.phi,puck.theta,metad.bias  FILEthe name of the file on which to output these quantities=COLVAR2
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=puck.phi,puck.amplitude,metad.bias  FILEthe name of the file on which to output these quantities=COLVAR3
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=puck.amplitude,puck.theta,metad.bias  FILEthe name of the file on which to output these quantities=COLVAR4


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