PLUMED-NEST-TEST-SITE

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=plumedEnables 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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=input-chignolin.pdb
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis 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 ENTITY0the atoms that make up a molecule that you wish to align=1-166

eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details
volThe VOLUME action with label vol calculates the following quantities:
 Quantity   
 Type   
 Description  
vol
scalar
the volume of simulation box: VOLUMECalculate the volume the simulation box. More details
pdb_rmsdThe RMSD action with label pdb_rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
pdb_rmsd
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa 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
pdb_rmsd: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa 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  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0

ecvThe ECV_MULTITHERMAL_MULTIBARIC action with label ecv calculates the following quantities:
 Quantity   
 Type   
 Description  
ecv.ene
scalar
the value of the argument named ene
ecv.vol
scalar
the value of the argument named vol: ECV_MULTITHERMAL_MULTIBARICExpand a simulation to sample multiple temperatures and pressures. This action has hidden defaults. More details ...
  ARGthe labels of the potential energy and of the volume of the system=ene,vol
# TEMP=500
  TEMP_MINthe minimum of the temperature range=270
  TEMP_MAXthe maximum of the temperature range=800
  PRESSUREpressure=0.06022140857*2000 #2 kbar
  PRESSURE_MINthe minimum of the pressure range=0.06022140857  #1 bar
  PRESSURE_MAXthe maximum of the pressure range=0.06022140857*4000 #4 kbar
  CUT_CORNERavoid region of high temperature and low pressure=500,0.06022140857,800,0.06022140857*1000
...
ecv: ECV_MULTITHERMAL_MULTIBARICExpand a simulation to sample multiple temperatures and pressures. This action uses the defaults shown here. More details ...
  ARGthe labels of the potential energy and of the volume of the system=ene,vol
# TEMP=500
  TEMP_MINthe minimum of the temperature range=270
  TEMP_MAXthe maximum of the temperature range=800
  PRESSUREpressure=0.06022140857*2000 #2 kbar
  PRESSURE_MINthe minimum of the pressure range=0.06022140857  #1 bar
  PRESSURE_MAXthe maximum of the pressure range=0.06022140857*4000 #4 kbar
  CUT_CORNERavoid region of high temperature and low pressure=500,0.06022140857,800,0.06022140857*1000
 TEMP temperature=-1
...
opesThe OPES_EXPANDED action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action has hidden defaults. More details ARGthe 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 PACEhow often the bias is updated=500 WALKERS_MPI switch on MPI version of multiple walkers
opes: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action uses the defaults shown here. More details ARGthe 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 PACEhow often the bias is updated=500 WALKERS_MPI switch on MPI version of multiple walkers  OBSERVATION_STEPS number of unbiased initial PACE steps to collect statistics for initialization=100 PRINT_STRIDE stride for printing to DELTAFS file, in units of PACE=100

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

PRINTPrint quantities to a file. More details FMTthe format that should be used to output real numbers=%g STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=Colvar.data ARGthe labels of the values that you would like to print to the file=ene,vol,pdb_rmsd,opes.*

ENDPLUMEDTerminate plumed input. More details

temp=500 K
pres=2000 bar

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