Project ID: plumID:24.012
Source: AFEC_YTH_example/plumed.dat
Originally used with PLUMED version: 2.9
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
tested on master
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
#LOAD FILE=./GHBFIX.cpp

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=system_afec.pdb

#group_all: GHBFIX PAIR GROUPA=311,2073,617 GROUPB=2610,2643,2529 D_0=0.2 D_MAX=0.3 C=0.8 TYPES=typesTable.dat PARAMS=scalingParameters.dat
group_all: GHBFIXCalculate the GHBFIX interaction energy between GROUPA and GROUPB More details PAIR Pair only 1st element of the 1st group with 1st element in the second, etc GROUPAFirst list of atoms=311,2073 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2614,2647 D_0the value of D_0 in the switching function=0.2 D_MAXthe value of D_MAX in the switching function=0.3 Cthe value of C in the switching function=0.8 TYPESthe value of TYPES in the switching function=typesTable.dat PARAMSthe value of PARAMS in the switching function=scalingParameters.dat

tot_1: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=group_all PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=tot_1 LABELa label for the action so that its output can be referenced in the input to other actions=all_1
#PRINT ARG=tot_1,all_1.bias STRIDE=250 FILE=check_ghbfix21.dat


center: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=2564-2566           # geometric center of the host molecule
water_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=2739-27521:3   # oxygen atom of the water molecules
n: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=center GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=water_group 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 R_0=0.45 D_MAX=0.75} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10  # radius: 0.6 nm

c1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=317-355,388-401,535-602,1341-1364,1400-1413,1431-1447,1508-1526,2129-2140 
c2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2559-2575
d: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,c2


METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=n
SIGMAthe widths of the Gaussian hills=0.05    # small SIGMA ensure that the Gaussian approaximate a delta function
HEIGHTthe heights of the Gaussian hills=5
PACEthe frequency for hill addition=1000
GRID_MINthe lower bounds for the grid=0     
GRID_MAXthe upper bounds for the grid=10     
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
BIASFACTORuse well tempered metadynamics and use this bias factor=3
LABELa label for the action so that its output can be referenced in the input to other actions=metad
FILE a file in which the list of added hills is stored=HILLS
#RESTART=YES
... METAD

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ...
 ARGthe arguments on which the bias is acting=n
 ATthe positions of the wall=2.5
 KAPPAthe force constant for the wall=200.0
 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=uwall
... UPPER_WALLS

LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ...
 ARGthe arguments on which the bias is acting=n
 ATthe positions of the wall=-0.1
 KAPPAthe force constant for the wall=200.0
 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=lwall
... LOWER_WALLS

DEBUGSet some debug options. More details DETAILED_TIMERS switch on detailed timers

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