PLUMED-NEST

Project ID: plumID:20.026
Source: plumed.dat
Originally used with PLUMED version: 2.5
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

rmsd_a: 
MULTI_RMSD
Calculate RMSD distances for different domains and combine them. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=OBP_lis_final.pdb 
TYPE
 the manner in which RMSD alignment is performed
=MULTI-OPTIMAL
rmsd_b: 
MULTI_RMSD
Calculate RMSD distances for different domains and combine them. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=OBP_lsd_final.pdb 
TYPE
 the manner in which RMSD alignment is performed
=MULTI-OPTIMAL
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=rmsd_a,rmsd_b  
AT
the position of the restraint
=0.375,0.425   
KAPPA
 specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=100000.0,100000.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=restraint
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rmsd_a,rmsd_b,restraint.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=COLVAR