Project ID: plumID:22.039
Source: glycine_plumed.dat
Originally used with PLUMED version: 2.6.1
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
LOADLoads a library, possibly defining new actions. More detailsFILE=InterFace.cppfile to be loadedLOADLoads a library, possibly defining new actions. More detailsFILE=PairOrientationalEntropy.cppfile to be loadedLOADLoads a library, possibly defining new actions. More detailsFILE=ManyAngle.cppfile to be loaded
# Define groups for the CV #INCLUDE FILE=centers.dat N: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=1-720:10 CA:the numerical indexes for the set of atoms in the groupGROUPDefine 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=2-720:10 C:the numerical indexes for the set of atoms in the groupGROUPDefine 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=3-720:10 O1:the numerical indexes for the set of atoms in the groupGROUPDefine 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=5-720:10 O:the numerical indexes for the set of atoms in the groupGROUPDefine 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=4-720:10 HA1:the numerical indexes for the set of atoms in the groupGROUPDefine 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=8-720:10 W:the numerical indexes for the set of atoms in the groupGROUPDefine 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=721-4321:3the numerical indexes for the set of atoms in the groupPAIR_ORIENTATIONAL_ENTROPY... LABEL=s1 #Should really be the geometric center, but will try just using the Ca position first CENTER=CA START=C END=N MAXR=0.6 SIGMA=0.05,0.25 ... PAIR_ORIENTATIONAL_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More detailsPAIR_ORIENTATIONAL_ENTROPY... LABEL=s2 CENTER=CA START=CA END=HA1 MAXR=0.6 SIGMA=0.05,0.125 #UP_DOWN_SYMMETRY ... PAIR_ORIENTATIONAL_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More details
# Define the CVMANY_ANGLE... LABEL=ma1 CENTER=CA START=C END=N RCUT=0.64 NOPBC MEAN MOMENT2 ... MANY_ANGLEThis action is not part of PLUMED and was included by using a LOAD command More detailsMANY_ANGLE... LABEL=ma2_6 CENTER=CA START=CA END=HA1 RCUT=0.64 NOPBC MEAN MOMENT2 ... MANY_ANGLEThis action is not part of PLUMED and was included by using a LOAD command More detailsCOORDINATIONNUMBER...Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsLABEL=cna label for the action so that its output can be referenced in the input to other actionsSPECIES=CAthis keyword is used for colvars such as coordination numberSWITCH={RATIONAL R_0=0.6 D_MAX=0.8}the switching function that it used in the construction of the contact matrixMORE_THAN1={RATIONAL R_0=8.0 D_MAX=9.0}calculate the number of variables that are more than a certain target valueMORE_THAN2={RATIONAL R_0=11.0 D_MAX=12.0}calculate the number of variables that are more than a certain target valueLOWMEM... COORDINATIONNUMBERthis flag does nothing and is present only to ensure back-compatibilityINTERFACE... LABEL=int CENTER=CA Water=W R0CUT=0.8 RWCUT=0.4 R_0=0.5 R_W=0.3 C_0=5 ... INTERFACEThis action is not part of PLUMED and was included by using a LOAD command More detailsQ4...Calculate fourth order Steinhardt parameters. More detailsLABEL=q4a label for the action so that its output can be referenced in the input to other actionsSPECIES=CAthis keyword is used for colvars such as coordination numberR_0=0.60The r_0 parameter of the switching functionMEANcalculate the mean of all the quantitiesLOWMEM... Q4this flag does nothing and is present only to ensure back-compatibilityQ6...Calculate sixth order Steinhardt parameters. More detailsLABEL=q6a label for the action so that its output can be referenced in the input to other actionsSPECIES=CAthis keyword is used for colvars such as coordination numberR_0=0.60The r_0 parameter of the switching functionMEANcalculate the mean of all the quantitiesLOWMEM... Q6this flag does nothing and is present only to ensure back-compatibility
l1_1:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=s1,s2,ma1.mean,ma1.moment2,ma2_6.mean,ma2_6.moment2,cn.morethan-1,cn.morethan-2,int,q4.mean,q6.meanthe input to this functionCOEFFICIENTS=0.268421709538,-0.165572479367,1.218452692032,-0.409345626831,-2.642394781113,1.740240216255,0.001185834059,0.033699873835,-0.008368298411,-0.443194448948,0.387469917536the coefficients of the arguments in your functionPERIODIC=NO l1_2:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=s1,s2,ma1.mean,ma1.moment2,ma2_6.mean,ma2_6.moment2,cn.morethan-1,cn.morethan-2,int,q4.mean,q6.meanthe input to this functionCOEFFICIENTS=-0.562040388584,-0.074013128877,-3.022350788116,1.183155536652,-0.754271864891,2.320541858673,-0.045729581267,-0.026172904298,-0.023710954934,0.582593202591,1.333106040955the coefficients of the arguments in your functionPERIODIC=NO l1r_1:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=l1_1the input to this functionFUNC=x+0.375591367483the function you wish to evaluatePERIODIC=NO l1r_2:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=l1_2the input to this functionFUNC=x+0.160054937005the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionMETAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=metada label for the action so that its output can be referenced in the input to other actionsARG=l1r_1,l1r_2the input for this action is the scalar output from one or more other actionsSIGMA=1.15,1.15the widths of the Gaussian hillsHEIGHT=5.0the heights of the Gaussian hillsBIASFACTOR=100use well tempered metadynamics and use this bias factorTEMP=300.0the system temperature - this is only needed if you are doing well-tempered metadynamicsPACE=1000the frequency for hill additionGRID_MIN=-10,-10the lower bounds for the gridGRID_MAX=10,10the upper bounds for the gridCALC_RCT... METADcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]Print quantities to a file. More detailsARG=s1,s2,ma1.mean,ma1.moment2,ma2_6.mean,ma2_6.moment2,cn.morethan-1,cn.morethan-2,int,q4.mean,q6.mean,l1r_1,l1r_2,metad.bias,metad.rbiasthe input for this action is the scalar output from one or more other actionsSTRIDE=100the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities