PLUMED-NEST

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

#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
The DISTANCE action with label d1 calculates a scalar quantityd2: 
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
The DISTANCE action with label d2 calculates a scalar quantityd3: 
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
The DISTANCE action with label d3 calculates a scalar quantityd4: 
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
The DISTANCE action with label d4 calculates a scalar quantityd5: 
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

The DISTANCE action with label d5 calculates a scalar quantity
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=Aindex
  
ARG
the 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
The DISTANCE action with label tm3-tm6_1 calculates a scalar quantitytm3-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
The DISTANCE action with label tm3-tm6_2 calculates a scalar quantityNPxxY: 
RMSD
Calculate the RMSD with respect to a reference structure. 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
The DISTANCE action with label yy calculates a scalar quantityPIF_a: 
RMSD
Calculate the RMSD with respect to a reference structure. 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

The DISTANCE action with label tm5 calculates a scalar quantitymeta: 
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
=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
The METAD action with label meta calculates the following quantities:
 Quantity   
 Description  
meta.bias
the instantaneous value of the bias potential
meta.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
meta.rct
the reweighting factor $c(t)$
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
=500 
FILE
the name of the file on which to output these quantities
=COLVAR