PLUMED-NEST

Project ID: plumID:22.033
Source: plumed.dat
Originally used with PLUMED version: 2.7
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

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
TIME
the units of time
=ps 
ENERGY
the units of energy
=kcal/mol
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
=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,17,18,20,21,22,23,24,25,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=COM_lig
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
=168,209,302,343,436,477,570,611,704,745,838,879,972,1013,1106,1147,1240,1281,1374,1415,1508,1549,1642,1683,1776,1817,1910,1951,2044,2085,2178,2219,2312,2353,2446,2487,2580,2621,2714,2755,2848,2889,2982,3023,3116,3157,3250,3291,3384,3425,3518,3559,3652,3693,3786,3827,3920,3961,4054,4095,4188,4229,4322,4363,4456,4497,4590,4631,4724,4765,4858,4899,4992,5033,5126,5167,5260,5301,5394,5435,5528,5569,5662,5703,5796,5837,5930,5971,6064,6105,6198,6239,6332,6373,6466,6507,6600,6641,6734,6775,6868,6909,7002,7043,7136,7177,7270,7311,7404,7445,7538,7579,7672,7713,7806,7847,7940,7981,8074,8115,8208,8249,8342,8383,8476,8517,8610,8651,8744,8785,8878,8919,9012,9053,9146,9187,9280,9321,9414,9455,9548,9589,9682,9723,9816,9857,9950,9991 
PHASES
 Compute center using trigonometric phases
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=COM_mem
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=COM_mem,COM_lig 
SCALED_COMPONENTS
 calculate the a, b and c scaled components of the distance separately and store them as label
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=COM_lig_dist
The DISTANCE action with label COM_lig_dist calculates the following quantities:
 Quantity   
 Description  
COM_lig_dist.a
the normalized projection on the first lattice vector of the vector connecting the two atoms
COM_lig_dist.b
the normalized projection on the second lattice vector of the vector connecting the two atoms
COM_lig_dist.c
the normalized projection on the third lattice vector of the vector connecting the two atoms
DRR
Used to performed extended-system adaptive biasing force(eABF) More details
 
ARG
the input for this action is the scalar output from one or more other actions
=COM_lig_dist.c 
FULLSAMPLES
 number of samples in a bin prior to application of the ABF
=200000 
GRID_MIN
the lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)
=-0.5 
GRID_MAX
the upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)
=0 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.001 
TEMP
the system temperature - needed when FRICTION is present
=310 
FRICTION
 add a friction to the variable, similar to extended Langevin Damping in Colvars
=8.0 
TAU
 specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars
=0.5 
TEXTOUTPUT
 use text output for grad and count files instead of boost::serialization binary output
 
OUTPUTFREQ
write results to a file every N steps
=2500000 
HISTORYFREQ
save history to a file every N steps
=25000000 
DRR_RFILE
specifies the restart file (
=drr_lo 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=drr_lo
The DRR action with label drr_lo calculates the following quantities:
 Quantity   
 Description  
drr_lo.bias
the instantaneous value of the bias potential
drr_lo._fict
one or multiple instances of this quantity can be referenced elsewhere in the input file
drr_lo._vfict
one or multiple instances of this quantity can be referenced elsewhere in the input file
drr_lo._biasforce
The bias force from eABF/DRR of the fictitious particle
drr_lo._springforce
Spring force between real CVs and extended CVs
drr_lo._fictNoPBC
the positions of fictitious particles (without PBC)
DRR
Used to performed extended-system adaptive biasing force(eABF) More details
 
ARG
the input for this action is the scalar output from one or more other actions
=COM_lig_dist.c 
FULLSAMPLES
 number of samples in a bin prior to application of the ABF
=200000 
GRID_MIN
the lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)
=0 
GRID_MAX
the upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)
=+0.5 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.001 
TEMP
the system temperature - needed when FRICTION is present
=310 
FRICTION
 add a friction to the variable, similar to extended Langevin Damping in Colvars
=8.0 
TAU
 specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars
=0.5 
TEXTOUTPUT
 use text output for grad and count files instead of boost::serialization binary output
 
OUTPUTFREQ
write results to a file every N steps
=2500000 
HISTORYFREQ
save history to a file every N steps
=25000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=drr_up
The DRR action with label drr_up calculates the following quantities:
 Quantity   
 Description  
drr_up.bias
the instantaneous value of the bias potential
drr_up._fict
one or multiple instances of this quantity can be referenced elsewhere in the input file
drr_up._vfict
one or multiple instances of this quantity can be referenced elsewhere in the input file
drr_up._biasforce
The bias force from eABF/DRR of the fictitious particle
drr_up._springforce
Spring force between real CVs and extended CVs
drr_up._fictNoPBC
the positions of fictitious particles (without PBC)
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
=drr_lo.COM_lig_dist.c_fict 
SIGMA
the widths of the Gaussian hills
=0.005 
HEIGHT
the heights of the Gaussian hills
=1.5 
PACE
the frequency for hill addition
=500 
GRID_MIN
the lower bounds for the grid
=-0.5 
GRID_MAX
the upper bounds for the grid
=+0.5 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.001 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=8 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310 
FILE
 a file in which the list of added hills is stored
=HILLS_lo 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad_lo
The METAD action with label metad_lo calculates the following quantities:
 Quantity   
 Description  
metad_lo.bias
the instantaneous value of the bias potential
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
=drr_up.COM_lig_dist.c_fict 
SIGMA
the widths of the Gaussian hills
=0.005 
HEIGHT
the heights of the Gaussian hills
=1.5 
PACE
the frequency for hill addition
=500 
GRID_MIN
the lower bounds for the grid
=-0.5 
GRID_MAX
the upper bounds for the grid
=+0.5 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.001 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=8 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310 
FILE
 a file in which the list of added hills is stored
=HILLS_up 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad_up
The METAD action with label metad_up calculates the following quantities:
 Quantity   
 Description  
metad_up.bias
the instantaneous value of the bias potential
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=COM_lig_dist.c 
FUNC
the function you wish to evaluate
=8e-3*step(-x)/(-x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=mirror_up
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=mirror_up 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uw_mirror
The BIASVALUE action with label uw_mirror calculates the following quantities:
 Quantity   
 Description  
uw_mirror.bias
the instantaneous value of the bias potential
uw_mirror._bias
one or multiple instances of this quantity can be referenced elsewhere in the input file
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=COM_lig_dist.c 
FUNC
the function you wish to evaluate
=8e-3*step(x)/x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=mirror_lo
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=mirror_lo 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lw_mirror
The BIASVALUE action with label lw_mirror calculates the following quantities:
 Quantity   
 Description  
lw_mirror.bias
the instantaneous value of the bias potential
lw_mirror._bias
one or multiple instances of this quantity can be referenced elsewhere in the input file
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
FILE
the name of the file on which to output these quantities
=plumed.log 
FMT
the format that should be used to output real numbers
=%12.4f
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=1000