Project ID: plumID:19.016
Source: 3.gamma_distortion/plumed.dat
Originally used with PLUMED version: 2.3
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#RESTART
ene : ENERGYCalculate the total potential energy of the simulation box. More details vol : VOLUMECalculate the volume of the simulation box. More details
cell : CELLCalculate the components of the simulation cell More details
aaa : COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cell.ax,cell.ay,cell.az POWERS the powers to which you are raising each of the arguments in your function=2,2,2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO bbb : COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cell.bx,cell.by,cell.bz POWERS the powers to which you are raising each of the arguments in your function=2,2,2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ccc : COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cell.cx,cell.cy,cell.cz POWERS the powers to which you are raising each of the arguments in your function=2,2,2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 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=cell.ax,cell.ay,cell.az,cell.bx,cell.by,cell.bz VARthe names to give each of the arguments in the function=ax,ay,az,bx,by,bz FUNCthe function you wish to evaluate=acos((ax*bx+ay*by+az*bz)/sqrt((ax*ax+ay*ay+az*az)*(bx*bx+by*by+bz*bz))) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=alpha ... MATHEVAL
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=cell.ax,cell.ay,cell.az,cell.cx,cell.cy,cell.cz VARthe names to give each of the arguments in the function=ax,ay,az,bx,by,bz FUNCthe function you wish to evaluate=acos((ax*bx+ay*by+az*bz)/sqrt((ax*ax+ay*ay+az*az)*(bx*bx+by*by+bz*bz))) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=beta ... MATHEVAL
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=cell.bx,cell.by,cell.bz,cell.cx,cell.cy,cell.cz VARthe names to give each of the arguments in the function=ax,ay,az,bx,by,bz FUNCthe function you wish to evaluate=acos((ax*bx+ay*by+az*bz)/sqrt((ax*ax+ay*ay+az*az)*(bx*bx+by*by+bz*bz))) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=gamma ... MATHEVAL
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=alpha,beta,gamma ATthe positions of the wall=1.7,2.0,1.7 KAPPAthe force constant for the wall=1000000,1000000,1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall #LOWER_WALLS ARG=alpha,gamma AT=1.5,1.5 KAPPA=1000000,1000000 LABEL=lwall LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=alpha,beta,gamma ATthe positions of the wall=1.5,1.3,1.5 KAPPAthe force constant for the wall=1000000,1000000,1000000 LABELa label for the action so that its output can be referenced in the input to other actions=lwall 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=beta SIGMAthe widths of the Gaussian hills=0.005 HEIGHTthe heights of the Gaussian hills=2.5 PACEthe frequency for hill addition=500 LABELa label for the action so that its output can be referenced in the input to other actions=metad TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 BIASFACTORuse well tempered metadynamics and use this bias factor=150
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=alpha,beta,gamma,aaa,bbb,ccc,ene,vol,metad.bias STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR