Project ID: plumID:23.005
Source: apo-5HT1A/plumed.dat
Originally used with PLUMED version: 2.5.3
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
tested onv2.10
tested onmaster
#RESTART
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
STRUCTURE
a file in pdb format containing a reference structure
=5ht1a_rec_ref.pdb
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
STRIDE
the frequency with which molecules are reassembled
=1
ENTITY0
the atoms that make up a molecule that you wish to align
=1-4932
d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=394,4660 d2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=770,1383 d3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=1457,1916 d4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=3028,3740 d5:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=4140,4352
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=Aindex
ARG
the values input to this function
=d1,d2,d3,d4,d5
VAR
the names to give each of the arguments in the function
=x,y,z,a,b
FUNC
the function you wish to evaluate
=((-14.43*x-7.62*y+9.11*z-6.32*a-5.22*b)+27.888
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO ... MATHEVAL
tm3-tm6_1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=3740,1574 tm3-tm6_2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=3665,1574 NPxxY:
RMSD
Calculate the RMSD with respect to a reference structure. This action has hidden defaults. More details
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=NPxxY_act_backbone_5ht1a.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL
yy:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=2903,4639 PIF_a:
RMSD
Calculate the RMSD with respect to a reference structure. This action has hidden defaults. More details
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=PIF_act_5ht1a.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL
tm5:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=2688,4468
meta:
METAD
Used to performed metadynamics on one or more collective variables. More details
ARG
the labels of the scalars on which the bias will act
=Aindex
SIGMA
the widths of the Gaussian hills
=0.1
HEIGHT
the heights of the Gaussian hills
=1
PACE
the frequency for hill addition
=500
FILE
a file in which the list of added hills is stored
=../HILLS
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5
GRID_MIN
the lower bounds for the grid
=-50
GRID_MAX
the upper bounds for the grid
=50
CALC_RCT
calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310
WALKERS_MPI
Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
PRINT
Print quantities to a file. More details
ARG
the labels of the values that you would like to print to the file
STRIDE
the frequency with which the quantities of interest should be output
=500
FILE
the name of the file on which to output these quantities
=COLVAR