PLUMED-NEST

Project ID: plumID:21.048
Source: plumed8.dat
Originally used with PLUMED version: 2.5
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 for metadynamics amber prod run 

# restart simulation (switch on after the first run to continue runs -reading from and appending to existing COLVAR and HILLS files)
#RESTART

# change distance/position units of I/O to Angstroms (default nm)
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A


# define virtual atom for centre of mass of lidocaine (=39atoms incl. H)
lqz: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=18531-18569

# define COM for point at base of vertical pore axis using CAatoms of 4x2x3 residues at bottom of each s5/6
ax_base: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=2222,2239,2258,4418,4437,4456,7107,7121,7140,8594,8613,8633,11313,11332,11351,13359,13378,13398,16676,16683,16702,18275,18292,18313

# define COM for point at top of vertical pore axis using CA of 4x6 residues on each P1
ax_top: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=3631,3641,3661,3680,3690,3709,7862,7873,7893,7912,7931,7947,12427,12434,12455,12474,12485,12504,17299,17310,17329,17348,17359,17378

# define COM for point to define the transverse axis using CA of 2x6 residues on P1 of DI/DII
ax_side: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=3631,3641,3661,3680,3690,3709,7862,7873,7893,7912,7931,7947

# Calculate distances of vectors between coms
d_ax: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=ax_top,ax_base
The DISTANCE action with label d_ax calculates a scalar quantitydtop_lqz: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=ax_top,lqz
The DISTANCE action with label dtop_lqz calculates a scalar quantitydbase_lqz: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=ax_base,lqz


# Calculate position based on the projection along the vertical pore axis
The DISTANCE action with label dbase_lqz calculates a scalar quantityz: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dtop_lqz,dbase_lqz,d_ax 
FUNC
the function you wish to evaluate
=(0.5*(y^2-x^2)/z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# Calculate perpendicular distance of lqz from the vertical pore axis
The CUSTOM action with label z calculates a scalar quantityr: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dtop_lqz,d_ax,z 
VAR
the names to give each of the arguments in the function
=x,z,o 
FUNC
the function you wish to evaluate
=(sqrt(x^2-(z/2-o)^2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# Calculate third positional parameter using torsional angle 
The CUSTOM action with label r calculates a scalar quantitytheta: 
TORSION
Calculate a torsional angle. More details
 
AXIS
two atoms that define an axis
=ax_top,ax_base 
VECTOR1
two atoms that define a vector
=ax_top,ax_side 
VECTOR2
two atoms that define a vector
=ax_base,lqz


# Add bias restraints to lqz position along s and z so it does not leave the pore interior
The TORSION action with label theta calculates a scalar quantityruwall: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=r 
AT
the positions of the wall
=18.0 
KAPPA
the force constant for the wall
=100 
EXP
 the powers for the walls
=2
The UPPER_WALLS action with label ruwall calculates the following quantities:
 Quantity   
 Description  
ruwall.bias
the instantaneous value of the bias potential
ruwall.force2
the instantaneous value of the squared force due to this bias potentialrlwall: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=r 
AT
the positions of the wall
=0.0 
KAPPA
the force constant for the wall
=100 
EXP
 the powers for the walls
=2 # Should not be necessary; but might help prevent GPU errors ?
The LOWER_WALLS action with label rlwall calculates the following quantities:
 Quantity   
 Description  
rlwall.bias
the instantaneous value of the bias potential
rlwall.force2
the instantaneous value of the squared force due to this bias potentialzlwall: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=z 
AT
the positions of the wall
=-12.0 
KAPPA
the force constant for the wall
=100 
EXP
 the powers for the walls
=2
The LOWER_WALLS action with label zlwall calculates the following quantities:
 Quantity   
 Description  
zlwall.bias
the instantaneous value of the bias potential
zlwall.force2
the instantaneous value of the squared force due to this bias potentialzuwall: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=z 
AT
the positions of the wall
=12.0 
KAPPA
the force constant for the wall
=100 
EXP
 the powers for the walls
=2

# activate metadynamics 3D gaussian using 3 colvars:
The UPPER_WALLS action with label zuwall calculates the following quantities:
 Quantity   
 Description  
zuwall.bias
the instantaneous value of the bias potential
zuwall.force2
the instantaneous value of the squared force due to this bias potentialmetad: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=z,r,theta ...
PACE
the frequency for hill addition
=500 
HEIGHT
the heights of the Gaussian hills
=1.0 # Deposit a Gaussian every 500 time steps (eq to 2ps), with initial height equal to 1.0kJoule/mol
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15.0 # Bias factor used for well-tempered MetaD ## Lower the biasf the greater hillheights reduction - use higher value for faster sampling; lower value for better convergence
SIGMA
the widths of the Gaussian hills
=0.5,0.5,0.1 # Specify gaussian widths for each colvar (based on fluctuations during unbiased runs)
FILE
 a file in which the list of added hills is stored
=HILLS # Gaussians will be written to file
GRID_MIN
the lower bounds for the grid
=-18,-1.9,-pi 
GRID_MAX
the upper bounds for the grid
=18,24,pi 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.2,0.2,0.04 # Gaussians will be stored on grid with respective min/max/binsizes for each colvar
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310 # Temperature of system (required for well-tempered MetaD)
WALKERS_N
number of walkers
=9 
WALKERS_ID
walker id
=8 
WALKERS_DIR
shared directory with the hills files from all the walkers
 
WALKERS_RSTRIDE
stride for reading hills files
=250 # Switch on Multiple Walkers MetaD with a total of 9 possible walkers, starting from walker#0; HILLS files read every 50steps=.2ps, written to DIR WHERE JOB WAS SUBMITTED
# CALC_RCT RCT_USTRIDE=250 # Compute the reweighting factor and rbias every 250 timesteps using for histogram analysis --requires hills to be stored on GRID
...


# Print values of the colvars and all bias potentials on separate COLVAR files for each walker
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=z,r,theta,*.bias 
FILE
the name of the file on which to output these quantities
=COLVAR.8 
STRIDE
 the frequency with which the quantities of interest should be output
=250