PLUMED-NEST-TEST-SITE

Project ID: plumID:19.078
Source: meta_reweigthing/6_D_adaptive/plumed.dat
Originally used with PLUMED version: 2.5-mod
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

# plumed input file
UNITSThis command sets the internal units for the code. More details NATURAL use natural units
The UNITS action with label  calculates somethingd1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1.x
scalar
the x-component of the vector connecting the two atoms
d1.y
scalar
the y-component of the vector connecting the two atoms
d1.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2.x
scalar
the x-component of the vector connecting the two atoms
d2.y
scalar
the y-component of the vector connecting the two atoms
d2.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,3 COMPONENTS calculate the x, y and z components of the distance separately and store them as label

ffThe MATHEVAL action with label ff calculates the following quantities:
 Quantity   
 Type   
 Description  
ff
scalar
an arbitrary function: 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=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z VARthe names to give each of the arguments in the function=x0,x1,x2,x3,x4,x5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=4.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2-1.0)^2-4.0*(x3-1.0)^2-4.0*(x4-1.0)^2-4.0*(x5-1.0)^2)+4.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2-1.0)^2-4.0*(x3+1.0)^2-4.0*(x4+1.0)^2-4.0*(x5+1.0)^2)+4.0*exp(-4.0*(x0+1.0)^2-4.0*(x1+1.0)^2-4.0*(x2+1.0)^2-4.0*(x3+1.0)^2-4.0*(x4+1.0)^2-4.0*(x5+1.0)^2)+4.0/(1.0/((5.0*x0+5.0)^2+(5.0*x1+5.0)^2+(5.0*x2+5.0)^2+(5.0*x3+5.0)^2+(5.0*x4+5.0)^2+(5.0*x5+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+(5.0*x3+5.0)^2+(5.0*x4+5.0)^2+(5.0*x5+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+(5.0*x3-5.0)^2+(5.0*x4-5.0)^2+(5.0*x5-5.0)^2+1)+1.0/((-2.04124145231931*x0-0.591751709536137*x1-0.591751709536137*x2-0.591751709536137*x3-0.591751709536137*x4+4.40824829046386*x5)^2.0+(-2.04124145231931*x0-0.591751709536137*x1-0.591751709536137*x2-0.591751709536137*x3+4.40824829046386*x4-0.591751709536137*x5)^2.0+(-2.04124145231931*x0-0.591751709536137*x1-0.591751709536137*x2+4.40824829046386*x3-0.591751709536137*x4-0.591751709536137*x5)^2.0+(-2.04124145231931*x0-0.591751709536137*x1+4.40824829046386*x2-0.591751709536137*x3-0.591751709536137*x4-0.591751709536137*x5)^2.0+(-2.04124145231931*x0+4.40824829046386*x1-0.591751709536137*x2-0.591751709536137*x3-0.591751709536137*x4-0.591751709536137*x5)^2.0+(0.408248290463863*x0+0.408248290463863*x1+0.408248290463863*x2+0.408248290463863*x3+0.408248290463863*x4+0.408248290463863*x5)^8.0)+1.0/((5.0*x3+5.0)^2.0+(5.0*x4+5.0)^2.0+(5.0*x5+5.0)^2.0+(-2.88675134594813*x0-1.05662432702594*x1+3.94337567297406*x2)^2.0+(-2.88675134594813*x0+3.94337567297406*x1-1.05662432702594*x2)^2.0+(0.577350269189626*x0+0.577350269189626*x1+0.577350269189626*x2)^8.0)+1.0/((5.0*x1-5.0)^2.0+(5.0*x2-5.0)^2.0+(0.577350269189626*x3+0.577350269189626*x4+0.577350269189626*x5)^8.0+(-2.88675134594813*x0-1.66666666666667*x3-1.66666666666667*x4+3.33333333333333*x5+2.88675134594813)^2.0+(-2.88675134594813*x0-1.66666666666667*x3+3.33333333333333*x4-1.66666666666667*x5+2.88675134594813)^2.0+(-2.88675134594813*x0+3.33333333333333*x3-1.66666666666667*x4-1.66666666666667*x5+2.88675134594813)^2.0))


bbThe BIASVALUE action with label bb calculates the following quantities:
 Quantity   
 Type   
 Description  
bb.bias
scalar
the instantaneous value of the bias potential
bb.ff_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named ff: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=ff

mtThe METAD action with label mt calculates the following quantities:
 Quantity   
 Type   
 Description  
mt.bias
scalar
the instantaneous value of the bias potential: 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=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z PACEthe frequency for hill addition=500
ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF
SIGMAthe widths of the Gaussian hills=400
SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.05,0.05,0.05,0.05,0.05,0.05
HEIGHTthe heights of the Gaussian hills=10.0 BIASFACTORuse well tempered metadynamics and use this bias factor=3 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=1
...
mt: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
ARGthe labels of the scalars on which the bias will act=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z PACEthe frequency for hill addition=500
ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF
SIGMAthe widths of the Gaussian hills=400
SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.05,0.05,0.05,0.05,0.05,0.05
HEIGHTthe heights of the Gaussian hills=10.0 BIASFACTORuse well tempered metadynamics and use this bias factor=3 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=1
 FILE a file in which the list of added hills is stored=HILLS
...


PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=mt.bias FILEthe name of the file on which to output these quantities=rr.bias_500 STRIDE the frequency with which the quantities of interest should be output=500
DUMPATOMSDump selected atoms on a file. More details STRIDE the frequency with which the atoms should be output=500 FILEfile on which to output coordinates; extension is automatically detected=traj.xyz ATOMSthe atom indices whose positions you would like to print out=1,2,3