PLUMED-NEST-TEST-SITE

Project ID: plumID:22.036
Source: plumed.dat
Originally used with PLUMED version: 2.5.6
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

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
# PDB that provides information on the molecules that are present in your system.
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=./GHBFIX.cpp

The LOAD action with label  calculates somethingMOLINFOThis 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=ref.pdb
#WHOLEMOLECULES ENTITY0=1-2026
# Flush open files regularly in case of data loss
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1000

#eRMSD_start: ...
#  ERMSD
#  ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16,@lcs-17,@lcs-18,@lcs-19,@lcs-20,@lcs-21,@lcs-22,@lcs-23,@lcs-24,@lcs-25,@lcs-26,@lcs-27,@lcs-28,@lcs-29,@lcs-30,@lcs-31,@lcs-32,@lcs-33,@lcs-34,@lcs-35,@lcs-36,@lcs-37,@lcs-38,@lcs-39,@lcs-40,@lcs-42,@lcs-43,@lcs-44,@lcs-45,@lcs-46,@lcs-47,@lcs-48,@lcs-49,@lcs-50,@lcs-51,@lcs-52,@lcs-53,@lcs-54,@lcs-55,@lcs-56,@lcs-57,@lcs-58,@lcs-59,@lcs-60,@lcs-61,@lcs-62,@lcs-63,@lcs-64
#  REFERENCE=ref.pdb
#...


####################################################################################################
# gHBfix RESTRAINT SECTION
####################################################################################################

# GroupA and GroupB are all relevant donors and acceptors. D_0, D_MAX and C have to be defined according to the gHBfix switching function - default values printed (Kuehrova, Mlynsky et al., JCTC 2019). Each relevant type of donor and acceptor are labeled with an integer (typesTable.dat) and eta/scaling parameters are specified (scalingParameters.dat).
group_1: 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=20,18,494,492,1036,1034,1503,1505,1508,240,242,244,274,272,1252,1254,1257,1288,1286 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1007,1005,1540,1538,2017,2015,523,525,527,779,781,784,1760,1758,1790,1792,1794,752,750 D_0the value of D_0 in the switching function=0.23 D_MAXthe value of D_MAX in the switching function=0.33 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

The GHBFIX action with label group_1 calculates the following quantities:
 Quantity   
 Description  
group_1.value
the GHBFIX interaction energy between the atoms in GROUPA and GROUPBtot_1: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=group_1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 

The COMBINE action with label tot_1 calculates the following quantities:
 Quantity   
 Description  
tot_1.value
a linear compbinationBIASVALUETakes 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



# Coordination number within middle base pairs as a CV
The BIASVALUE action with label all_1 calculates the following quantities:
 Quantity   
 Description  
all_1.bias
the instantaneous value of the bias potential
all_1._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filebp8_25: 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=233-244,773-787
The GROUP action with label bp8_25 calculates somethingbp9_56: 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=263-276,1751-1764
The GROUP action with label bp9_56 calculates somethingbp24_41: 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=741-754,1279-1292
The GROUP action with label bp24_41 calculates somethingbp57_40: 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=1246-1260,1783-1794

The GROUP action with label bp57_40 calculates somethingh12: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=bp8_25 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=bp9_56 R_0The r_0 parameter of the switching function=0.3 NN The n parameter of the switching function =4
The COORDINATION action with label h12 calculates the following quantities:
 Quantity   
 Description  
h12.value
the value of the coordinationh34: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=bp24_41 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=bp57_40 R_0The r_0 parameter of the switching function=0.3 NN The n parameter of the switching function =4
The COORDINATION action with label h34 calculates the following quantities:
 Quantity   
 Description  
h34.value
the value of the coordinationh13: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=bp8_25 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=bp24_41 R_0The r_0 parameter of the switching function=0.3 NN The n parameter of the switching function =4
The COORDINATION action with label h13 calculates the following quantities:
 Quantity   
 Description  
h13.value
the value of the coordinationh24: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=bp9_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=bp57_40 R_0The r_0 parameter of the switching function=0.3 NN The n parameter of the switching function =4

# Function to CVs that unifies the Gaussian width
The COORDINATION action with label h24 calculates the following quantities:
 Quantity   
 Description  
h24.value
the value of the coordinations12: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=h12 FUNCthe function you wish to evaluate=x^0.65 
The CUSTOM action with label s12 calculates the following quantities:
 Quantity   
 Description  
s12.value
an arbitrary functions34: CUSTOMCalculate a combination of variables using a custom expression. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=h34 FUNCthe function you wish to evaluate=x^0.65
#s13: CUSTOM PERIODIC=NO ARG=h13 FUNC=x^0.65
#s24: CUSTOM PERIODIC=NO ARG=h24 FUNC=x^0.65

#isoi: CUSTOM ARG=s12,s34 FUNC=x+y PERIODIC=NO
#isoi_1: CUSTOM ARG=s12,s34 FUNC=x-y PERIODIC=NO

# Set wall to restraint CV space
#LOWER_WALLS ARG=isoi_1 AT=0 KAPPA=0.22 LABEL=lwall
The CUSTOM action with label s34 calculates the following quantities:
 Quantity   
 Description  
s34.value
an arbitrary functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=h13,h24 ATthe positions of the wall=10,10 KAPPAthe force constant for the wall=0.02,0.02 LABELa label for the action so that its output can be referenced in the input to other actions=uwall

# Well-tempered MetaDynamics
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 potentialmetad: ...
  METADUsed to performed metadynamics on one or more collective variables. More details
  ARGthe labels of the scalars on which the bias will act=s12,s34
  PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=2.5 BIASFACTORuse well tempered metadynamics and use this bias factor=15
  SIGMAthe widths of the Gaussian hills=0.8,0.8
  FILE a file in which the list of added hills is stored=HILLS GRID_MINthe lower bounds for the grid=0,0 GRID_MAXthe upper bounds for the grid=26,26
  GRID_WSTRIDEwrite the grid to a file every N steps=25000000 GRID_WFILEthe file on which to write the grid=GRID GRID_RFILEa grid file from which the bias should be read at the initial step of the simulation=GRID
...

#DEBUG DETAILED_TIMERS

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=h12,h34,s12,s34,metad.bias 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=tot_1,all_1.bias STRIDE the frequency with which the quantities of interest should be output=2500 FILEthe name of the file on which to output these quantities=check_gHBfix_one-zero.dat