PLUMED-NEST

Project ID: plumID:20.022
Source: chignolin/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 multithermal-multibaric simulation that  #
#  samples a whole range of temperatures and pressures, using a    #
#  chosen fixed number of replicas (multiple walkers)              #
#                                                                  #
#++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#

#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
=input-chignolin.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
=1-166

ene: 
ENERGY
Calculate the total potential energy of the simulation box. More details
vol: 
VOLUME
Calculate the volume of the simulation box. More details
The VOLUME action with label vol calculates a scalar quantitypdb_rmsd: 
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
=input-chignolin.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL

ecv: 
ECV_MULTITHERMAL_MULTIBARIC
Expand a simulation to sample multiple temperatures and pressures. More details
 ...
  
ARG
the labels of the potential energy and of the volume of the system
=ene,vol
# TEMP=500
  
TEMP_MIN
the minimum of the temperature range
=270
  
TEMP_MAX
the maximum of the temperature range
=800
  
PRESSURE
pressure
=0.06022140857*2000 #2 kbar
  
PRESSURE_MIN
the minimum of the pressure range
=0.06022140857  #1 bar
  
PRESSURE_MAX
the maximum of the pressure range
=0.06022140857*4000 #4 kbar
  
CUT_CORNER
avoid region of high temperature and low pressure
=500,0.06022140857,800,0.06022140857*1000
...
The ECV_MULTITHERMAL_MULTIBARIC 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 
WALKERS_MPI
 switch on MPI version of multiple walkers

#e2e: DISTANCE ATOMS=5,147 #first and last CA
#gyr: GYRATION ATOMS=5,26,47,67,73,88,102,109,123,147

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
=ene,vol,pdb_rmsd,opes

ENDPLUMED
Terminate plumed input. More details


temp=500 K
pres=2000 bar

input obtained from unbiased simultation, only rep 6,8,9 start from folded