Project ID: plumID:25.000
Source: plumed-funcpathgeneral.dat
Originally used with PLUMED version: 2.8.1
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. RESTARTActivate restart. More details 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=protein.whole.pdb protein: 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=1-30956 WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=protein STRIDE the frequency with which molecules are reassembled=1 sd1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=8998-12265 sd2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=29083-29264 sd3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=29254-29422 sd4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2334-5958 arp3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-6581 arp2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=6582-12785 arpc1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=12786-18502 arpc2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=18503-23042 arpc4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=25870-28670 arpc3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=23043-25869 arpc5: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=28671-30956 d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=sd1,sd4 d2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=arp2,arpc3 d3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=arp3,arpc4 d4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=arpc1,arpc3 d5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=arpc3,arpc4 d6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=arpc3,arpc5 pp: FUNCPATHGENERALThis function calculates path collective variables (PCVs) using an arbitrary combination of collective variables. More details COLUMNSList of columns in the reference colvar file specifying the CVs=1,2,3,4 ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4 COEFFICIENTSCoefficients to be assigned to the CVs=1,1,1,1 REFERENCEColvar file needed to provide the CV milestones=COLVAR_PATH1 LAMBDALambda parameter required for smoothing=28 metad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=pp.s SIGMAthe widths of the Gaussian hills=0.5 HEIGHTthe heights of the Gaussian hills=1 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 GRID_MINthe lower bounds for the grid=-1 GRID_MAXthe upper bounds for the grid=12 GRID_BINthe number of bins for the grid=120 BIASFACTORuse well tempered metadynamics and use this bias factor=100 GRID_NOSPLINE don't use spline interpolation with grids PACEthe frequency for hill addition=5000 FILE a file in which the list of added hills is stored=HILLS CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] uwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.z ATthe positions of the wall=0.2 KAPPAthe force constant for the wall=100000.0 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 #lwall: LOWER_WALLS ARG=pp.z AT=-0.2 KAPPA=100000.0 EXP=2 EPS=1 OFFSET=0 #dwall: UPPER_WALLS ARG=d1 AT=5.4 KAPPA=10000.0 EXP=2 EPS=1 OFFSET=0 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=pp.s,pp.z,d1,d2,d3,d4,d5,d6,metad.bias,uwall.bias,metad.rbias STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=colvar1