Project ID: plumID:20.007
Source: double/plumed.dat
Originally used with PLUMED version: 2.4.2
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
tested onv2.10
tested onmaster
RESTARTActivate restart. More details
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=1-2640

d686_1739: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=686,1739
d1834_1853: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1834,1853
d1732_1739: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1732,1739
d1755_1765: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1755,1765
d1823_1834: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1823,1834
d1765_1823: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1765,1823
d1809_1877: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1809,1877
d1187_1739: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1187,1739
d1877_1894: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1877,1894
d1853_1947: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1853,1947

psi: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1773,1775,1791,1793
dist: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1772,1822 # A1130-S117H

rmsd: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=rmsd.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
COMBINECalculate a polynomial combination of a set of other variables. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=rc1 ARGthe values input to this function=d686_1739,d1834_1853,d1732_1739,d1755_1765,d1823_1834,d1765_1823,d1809_1877,d1187_1739,d1877_1894,d1853_1947 COEFFICIENTS the coefficients of the arguments in your function=0.135,-0.343,0.432,0.348,-0.377,0.162,-0.138,0.294,0.527,-0.070 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... COMBINE
COMBINECalculate a polynomial combination of a set of other variables. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=rc2 ARGthe values input to this function=d686_1739,d1834_1853,d1732_1739,d1755_1765,d1823_1834,d1765_1823,d1809_1877,d1187_1739,d1877_1894,d1853_1947 COEFFICIENTS the coefficients of the arguments in your function=-0.075,-0.226,0.758,0.083,-0.326,0.247,-0.173,-0.137,0.194,0.330 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... COMBINE
METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=metad ARGthe labels of the scalars on which the bias will act=rc1,rc2 PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.5 SIGMAthe widths of the Gaussian hills=0.021,0.014 BIASFACTORuse well tempered metadynamics and use this bias factor=10.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 ... METAD
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd ATthe positions of the wall=.4 KAPPAthe force constant for the wall=10000.0 EXP the powers for the walls=4 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d686_1739,d1834_1853,d1732_1739,d1755_1765,d1823_1834,d1765_1823,d1809_1877,d1187_1739,d1877_1894,d1853_1947,rc1,rc2,psi,dist,rmsd,uwall.bias,metad.bias STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=COLVAR_full