**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

# vim:ft=plumed# PDB that provides information on the molecules that are present in your system.Enables syntax highlighting for PLUMED files in vim. See here for more details.LOADLoads a library, possibly defining new actions. More detailsFILE=./GHBFIX.cppfile to be loadedMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=ref.pdb #WHOLEMOLECULES ENTITY0=1-2026 # Flush open files regularly in case of data lossa file in pdb format containing a reference structureFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1000the frequency with which all the open files should be flushed

#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 among GROUPA and GROUPB More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcGROUPA=20,18,494,492,1036,1034,1503,1505,1508,240,242,244,274,272,1252,1254,1257,1288,1286First list of atomsGROUPB=1007,1005,1540,1538,2017,2015,523,525,527,779,781,784,1760,1758,1790,1792,1794,752,750Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.23the value of D_0 in the switching functionD_MAX=0.33the value of D_MAX in the switching functionC=0.8the value of C in the switching functionTYPES=typesTable.datthe value of TYPES in the switching functionPARAMS=scalingParameters.datthe value of PARAMS in the switching functiontot_1:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input for this action is the scalar output from one or more other actionsgroup_1PERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionBIASVALUETakes the value of one variable and use it as a bias More detailsARG=the input for this action is the scalar output from one or more other actionstot_1LABEL=a label for the action so that its output can be referenced in the input to other actionsall_1

# Coordination number within middle base pairs as a CVbp8_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 detailsATOMS=233-244,773-787the numerical indexes for the set of atoms in the groupbp9_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 detailsATOMS=263-276,1751-1764the numerical indexes for the set of atoms in the groupbp24_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 detailsATOMS=741-754,1279-1292the numerical indexes for the set of atoms in the groupbp57_40:ATOMS=1246-1260,1783-1794the numerical indexes for the set of atoms in the grouph12:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsbp8_25GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)bp9_56R_0=0.3The r_0 parameter of the switching functionNN=4The n parameter of the switching functionh34:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsbp24_41GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)bp57_40R_0=0.3The r_0 parameter of the switching functionNN=4The n parameter of the switching functionh13:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsbp8_25GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)bp24_41R_0=0.3The r_0 parameter of the switching functionNN=4The n parameter of the switching functionh24:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsbp9_56GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)bp57_40R_0=0.3The r_0 parameter of the switching functionNN=4The n parameter of the switching function

# Function to CVs that unifies the Gaussian widths12:CUSTOMCalculate a combination of variables using a custom expression. More detailsPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionARG=the input for this action is the scalar output from one or more other actionsh12FUNC=x^0.65the function you wish to evaluates34:CUSTOMCalculate a combination of variables using a custom expression. More detailsPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionARG=the input for this action is the scalar output from one or more other actionsh34FUNC=x^0.65 #s13: CUSTOM PERIODIC=NO ARG=h13 FUNC=x^0.65 #s24: CUSTOM PERIODIC=NO ARG=h24 FUNC=x^0.65the function you wish to evaluate

#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=lwallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsh13,h24AT=10,10the positions of the wallKAPPA=0.02,0.02the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall

# Well-tempered MetaDynamicsmetad: ...METADUsed to performed metadynamics on one or more collective variables. More detailsARG=the input for this action is the scalar output from one or more other actionss12,s34PACE=500the frequency for hill additionHEIGHT=2.5the heights of the Gaussian hillsBIASFACTOR=15use well tempered metadynamics and use this bias factorSIGMA=0.8,0.8the widths of the Gaussian hillsFILE=HILLSa file in which the list of added hills is storedGRID_MIN=0,0the lower bounds for the gridGRID_MAX=26,26the upper bounds for the gridGRID_WSTRIDE=25000000write the grid to a file every N stepsGRID_WFILE=GRIDthe file on which to write the gridGRID_RFILE=GRID ...a grid file from which the bias should be read at the initial step of the simulation

#DEBUG DETAILED_TIMERSPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsh12,h34,s12,s34,metad.biasSTRIDE=500the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionstot_1,all_1.biasSTRIDE=2500the frequency with which the quantities of interest should be outputFILE=check_gHBfix_one-zero.datthe name of the file on which to output these quantities