Project ID: plumID:24.028
Source: inputs/tip3p/quadruplex/metadyn/plumed_metad.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
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# Activate MOLINFO functionalities 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=../conf.pdb rna: 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 NDX_FILEthe name of index file (gromacs syntax)=../indices.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Quad_core rnacenter: 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=rna posrna: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=rnacenter memb: 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 NDX_FILEthe name of index file (gromacs syntax)=../indices.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=C116 membcenter: 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=memb posmemb: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=membcenter d: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=rnacenter,membcenter SCALED_COMPONENTS calculate the a, b and c scaled components of the distance separately and store them as label scaled_zdist: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d.c COEFFICIENTS the coefficients of the arguments in your function=10.1512 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-5.0756,5.0756 glayer1: 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 NDX_FILEthe name of index file (gromacs syntax)=../indices.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Glayer1 glayer1_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=glayer1 glayer2: 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 NDX_FILEthe name of index file (gromacs syntax)=../indices.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Glayer2 glayer2_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=glayer2 d_kv: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=glayer1_center,glayer2_center COMPONENTS calculate the x, y and z components of the distance separately and store them as label mod_d_kv: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=glayer1_center,glayer2_center costheta: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=d_kv.z,mod_d_kv VARthe names to give each of the arguments in the function=x,y FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO dist_k: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=639,640 wall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dist_k ATthe positions of the wall=0.42 KAPPAthe force constant for the wall=15000 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 metad: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ... ARGthe labels of the scalars on which the bias will act=scaled_zdist,costheta SIGMAthe widths of the Gaussian hills=0.05,0.05 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=11.25 PACEthe frequency for hill addition=200 BIASFACTORuse well tempered metadynamics and use this bias factor=10 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=323 GRID_MINthe lower bounds for the grid=-5.0756,-1 GRID_MAXthe upper bounds for the grid=5.0756,1 ...
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=scaled_zdist,costheta,metad.bias,wall.bias FILEthe name of the file on which to output these quantities=METADYN STRIDE the frequency with which the quantities of interest should be output=10000