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
tested onv2.8
tested onmaster
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
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
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
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
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
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
=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
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
=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
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