PLUMED-NEST

Project ID: plumID:20.022
Source: alanine/plumed.dat
Originally used with PLUMED version: 2.8
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#
#                                                                 #
#  This input generates a multicanonical simulation that samples  #
#  the temperature range 300K-1000K in a single simulation        #
#                                                                 #
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#

phi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15
The TORSION action with label phi calculates a scalar quantitypsi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17
The TORSION action with label psi calculates a scalar quantityene: 
ENERGY
Calculate the total potential energy of the simulation box. More details

ecv: 
ECV_MULTITHERMAL
Expand a simulation to sample multiple temperatures simultaneously. More details
 
ARG
the label of the internal energy of the system
=ene 
TEMP_MAX
the maximum of the temperature range
=1000 #TEMP_STEPS=1000
The ECV_MULTITHERMAL action with label ecv calculates a scalar quantityopes: 
OPES_EXPANDED
On-the-fly probability enhanced sampling with expanded ensembles for the target distribution. More details
 
ARG
the label of the ECVs that define the expansion
=ecv 
FILE
 a file with the estimate of the relative Delta F for each component of the target and of the global c(t)
=DeltaFs.data 
PACE
how often the bias is updated
=500

The OPES_EXPANDED action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
FMT
the format that should be used to output real numbers
=%g 
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.data 
ARG
the input for this action is the scalar output from one or more other actions
=phi,psi,ene,opes

ENDPLUMED
Terminate plumed input. More details


The simulation with OPES well-tempered used for Fig.S1 was taken from the paper https://pubs.acs.org/doi/10.1021/acs.jpclett.0c00497

The option TEMP_STEPS=1000 was used to make Fig.S2 of the supplemental material.
Default geometric spacing of the temperature steps was introduced in a later version of the code,
thus to obtain the same simulations of the paper also the keyword NO_GEOM_SPACING should be added.