PLUMED-NEST-TEST-SITE

Project ID: plumID:19.037
Source: Walker_1/plumed.mtd.inp
Originally used with PLUMED version: 2.3
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

RESTARTActivate restart. More details

# Units
The RESTART action with label  calculates somethingUNITSThis command sets the internal units for the code. More details ENERGYthe units of energy=eV LENGTHthe units of lengths=A TIMEthe units of time=ps

# CV(s)

d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,52
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=24,67

v1The DISTANCE action with label v1 calculates the following quantities:
 Quantity   
 Type   
 Description  
v1.x
scalar
the x-component of the vector connecting the two atoms
v1.y
scalar
the y-component of the vector connecting the two atoms
v1.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=8,16 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
v2The DISTANCE action with label v2 calculates the following quantities:
 Quantity   
 Type   
 Description  
v2.x
scalar
the x-component of the vector connecting the two atoms
v2.y
scalar
the y-component of the vector connecting the two atoms
v2.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=21,16 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
v3The DISTANCE action with label v3 calculates the following quantities:
 Quantity   
 Type   
 Description  
v3.x
scalar
the x-component of the vector connecting the two atoms
v3.y
scalar
the y-component of the vector connecting the two atoms
v3.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=51,59 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
v4The DISTANCE action with label v4 calculates the following quantities:
 Quantity   
 Type   
 Description  
v4.x
scalar
the x-component of the vector connecting the two atoms
v4.y
scalar
the y-component of the vector connecting the two atoms
v4.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=64,59 COMPONENTS calculate the x, y and z components of the distance separately and store them as label

fxThe MATHEVAL action with label fx calculates the following quantities:
 Quantity   
 Type   
 Description  
fx
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=v1.y,v1.z,v2.y,v2.z VARthe names to give each of the arguments in the function=ay,az,by,bz FUNCthe function you wish to evaluate=ay*bz-az*by PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-24.9215,24.9215
fyThe MATHEVAL action with label fy calculates the following quantities:
 Quantity   
 Type   
 Description  
fy
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=v1.x,v1.z,v2.x,v2.z VARthe names to give each of the arguments in the function=ax,az,bx,bz FUNCthe function you wish to evaluate=az*bx-ax*bz PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-24.9215,24.9215
fzThe MATHEVAL action with label fz calculates the following quantities:
 Quantity   
 Type   
 Description  
fz
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=v1.x,v1.y,v2.x,v2.y VARthe names to give each of the arguments in the function=ax,ay,bx,by FUNCthe function you wish to evaluate=ax*by-ay*bx PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-24.9215,24.9215

gxThe MATHEVAL action with label gx calculates the following quantities:
 Quantity   
 Type   
 Description  
gx
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=v3.y,v3.z,v4.y,v4.z VARthe names to give each of the arguments in the function=ay,az,by,bz FUNCthe function you wish to evaluate=ay*bz-az*by PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-24.9215,24.9215
gyThe MATHEVAL action with label gy calculates the following quantities:
 Quantity   
 Type   
 Description  
gy
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=v3.x,v3.z,v4.x,v4.z VARthe names to give each of the arguments in the function=ax,az,bx,bz FUNCthe function you wish to evaluate=az*bx-ax*bz PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-24.9215,24.9215
gzThe MATHEVAL action with label gz calculates the following quantities:
 Quantity   
 Type   
 Description  
gz
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=v3.x,v3.y,v4.x,v4.y VARthe names to give each of the arguments in the function=ax,ay,bx,by FUNCthe function you wish to evaluate=ax*by-ay*bx PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-24.9215,24.9215

MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=thetaThe MATHEVAL action with label theta calculates the following quantities:
 Quantity   
 Type   
 Description  
theta
scalar
an arbitrary function
ARGthe values input to this function=fx,fy,fz,gx,gy,gz
VARthe names to give each of the arguments in the function=ax,ay,az,bx,by,bz
FUNCthe function you wish to evaluate=(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=-2,2
... MATHEVAL

# Walls
uwall1The UPPER_WALLS action with label uwall1 calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall1.bias
scalar
the instantaneous value of the bias potential
uwall1.force2
scalar
the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=22.0 KAPPAthe force constant for the wall=1000 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
uwall2The UPPER_WALLS action with label uwall2 calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall2.bias
scalar
the instantaneous value of the bias potential
uwall2.force2
scalar
the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d2 ATthe positions of the wall=22.0 KAPPAthe force constant for the wall=1000 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

# Metadynamics
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=mtdThe METAD action with label mtd calculates the following quantities:
 Quantity   
 Type   
 Description  
mtd.bias
scalar
the instantaneous value of the bias potential
  ARGthe labels of the scalars on which the bias will act=d1,d2,theta
  SIGMAthe widths of the Gaussian hills=0.2,0.2,0.05
  PACEthe frequency for hill addition=1000
  HEIGHTthe heights of the Gaussian hills=0.026
  BIASFACTORuse well tempered metadynamics and use this bias factor=5 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
  WALKERS_DIRshared directory with the hills files from all the walkers=../HILLS_DIR 
  WALKERS_RSTRIDEstride for reading hills files=500 
  WALKERS_Nnumber of walkers=2
  WALKERS_IDwalker id=1
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=mtd
  ARGthe labels of the scalars on which the bias will act=d1,d2,theta
  SIGMAthe widths of the Gaussian hills=0.2,0.2,0.05
  PACEthe frequency for hill addition=1000
  HEIGHTthe heights of the Gaussian hills=0.026
  BIASFACTORuse well tempered metadynamics and use this bias factor=5 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
  WALKERS_DIRshared directory with the hills files from all the walkers=../HILLS_DIR 
  WALKERS_RSTRIDEstride for reading hills files=500 
  WALKERS_Nnumber of walkers=2
  WALKERS_IDwalker id=1
 FILE a file in which the list of added hills is stored=HILLS
... METAD

# Print CV
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,theta,uwall1.bias,uwall2.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=1
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1000