Project ID: plumID:23.037
Source: SBP_plumed_nest/Plumed_files/GGTGG/plumed.dat
Originally used with PLUMED version: 2.6
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
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#RESTART
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=GGTGG.pdb ace: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2257-2262 G1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2263-2269 G2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2270-2276 AA: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2281-2288 G4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2291-2297 G5: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2298-2304 nme: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2305-2310 surf: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=38,49,52,54,56,59,62,65,67,69,72,74,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,946 dace: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,ace COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dG1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,G1 COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dG2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,G2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dAA: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,AA COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dG4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,G4 COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dG5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,G5 COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances dnme: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=surf,nme COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dace.z ATthe positions of the wall=4.0 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dace UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dnme.z ATthe positions of the wall=4.0 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dnme UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dG1.z ATthe positions of the wall=4.0 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dG1 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dG2.z ATthe positions of the wall=4.0 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dG2 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dAA.z ATthe positions of the wall=4.0 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dAA UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dG4.z ATthe positions of the wall=4.0 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dG4 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dG5.z ATthe positions of the wall=4.0 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_dG5
PBMETADUsed to performed Parallel Bias metadynamics. More details ... WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR ARGthe labels of the scalars on which the bias will act=dace.z,dnme.z,dG1.z,dG2.z,dAA.z,dG4.z,dG5.z SIGMAthe widths of the Gaussian hills=200.0 ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.01,0.01,0.01,0.01,0.01,0.01,0.01 SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=1.0,1.0,1.0,1.0,1.0,1.0,1.0 HEIGHTthe height of the Gaussian hills, one for all biases=1.2 #kJ/mol PACEthe frequency for hill addition, one for all biases=500 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=20 # Sqrt[cv]*8 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298.0 LABELa label for the action so that its output can be referenced in the input to other actions=PBMETAD GRID_MINthe lower bounds for the grid=-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5 GRID_MAXthe upper bounds for the grid=5.0,5.0,5.0,5.0,5.0,5.0,5.0 FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=../HILLS.ace,../HILLS.dnme,../HILLS.dG1,../HILLS.dG2,../HILLS.dAA,../HILLS.dG4,../HILLS.dG5 ... PBMETAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dace.z,dnme.z,dG1.z,dG2.z,dAA.z,dG4.z,dG5.z,PBMETAD.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