# Folder fo look for files with relative paths
workingFolder {/simulations/test_steered_simulation}
# Configuration file name
configFileName {update_parameters_conf.txt}
# Status file name
statusFileName {prmtr_sim_status.txt}
# Protein structure file
structure {test_steered_simulation.psf}
# Protein coordinates
coordinates {test_steered_simulation_temp.coor}
# Coordinates File type
# coordinatesFileType pdb
coordinatesFileType namdbin
# coordinatesFileType dcd
# Reference coordinates - used for various calculations as a staedy reference point
referenceCoordinates {test_steered_simulation_final.pdb}
# Reference Coordinates File type
referenceCoordinatesFileType pdb
# referenceCoordinatesFileType namdbin
# referenceCoordinatesFileType dcd
# Input spring constant coefficients file name
constantsFileName {test_steered_simulation_cnst.pdb}
# Output coordinates file name
outputCoordinatesFileName {test_steered_simulation_tgt.pdb}
# Output spring constant coefficients file name, pdb type only
outputConstantsFileName {test_steered_simulation_cnst.pdb}
# Input spring constant coefficients column
constantsColumn x
# Selection for atoms which should be dynamically restrained - i.e. for which all these calculations are performed
# selectionText "backbone and resid 27 to 90"
# selectionText "backbone"
# selectionText {{residue 3} {residue 7} {residue 11} {residue 15}}
# selectionText "backbone and resid 121 124"
selectionText {{backbone and resid 121 and fragment 0} {backbone and resid 124 and fragment 0} {backbone and resid 121 and fragment 1} {backbone and resid 124 and fragment 1} {backbone and resid 121 and fragment 2} {backbone and resid 124 and fragment 2} {backbone and resid 121 and fragment 3} {backbone and resid 124 and fragment 3} {backbone and resid 121 and fragment 4} {backbone and resid 124 and fragment 4}}
# Second Selection for atoms which should be dynamically restrained - i.e. for which all these calculations are performed. It is used in complex restraints
selection2Text "index 1000000"
# Option to average among time frames 1 - yes, 0 - no
timeAveraging 0
# Option to choose the real frame closest to an average (by rmsd) as an average frame 1 - yes, 0 - no
realFrame 0
# Option to Save time-averaged structure
saveTimeAveragedStructure 0
# start frame for time averaging. If < 0, then this frame is relative to the last frame
firstFrame 0
# Last frame for time averaging. If -1, then the very last frame
lastFrame -1
# If <1>, Read spring constants from the existing file, calculate new constants, assign them and leave all old constants, which were not reassigned, in place. Useful when there are some additional harmonic restraints in the system, not related to parametryzation. If <0> - set all the coefficients except newly calculated, to 0.
preserveUnassignedConstants 0
# If <1>, Read Target coordinates from the existing file, calculate new target coordinates, assign them and leave all old coordinates, which were not reassigned, in place. Useful when there are some additional harmonic restraints in the system, not related to parametryzation. If <0> - set all the coordinates except newly calculated, to 0. If <-1> - coordinates from the current protein snapshot will be inserted into unassigned target coordinate positions
preserveUnassignedTargets 0
# <1> - Independent initial spring constants for every atom. Then they scale according to constantsScaleMode. <0> - equal initial spring constants for all the restrained atoms. Then they scale according to constantsScaleMode.
independentConstants 0
# Mode of the target coordinates calculation
# <0> - "fixed target" mode : no target update
# <1> - "cylindrical projection target" : target points are mapped onto cyllinder of predefined (in u"pdate_parameters.vmd" script) radius. They have the same angular coordinates as in the input coordinates file
# <2> - "constant force outward" : all the restrained atoms get the same amount of force in the direction from the central (z) axis through the atom.
# <3> - "Coriolis force" : all the restrained atoms get the force propotional to the square of the distance to the central axis. Force will be in the direction from the central (z) axis through the atom
# <4> - "constant shift" : target coordinate of the atom shifts every time in radial direction by the fixed distance relative to the current coordinate of the atom
# <5> - "cylindrical projection (selection 1) and axis (selection 2) target" : target points are mapped onto cyllinder of predefined (in the "update_parameters.vmd" script) radius. They have the same angular coordinates as in the input coordinates file
# <6> - "constant force outward (selection 1) and axis (selection 2)" : all the restrained atoms get the same amount of force in the direction from the central (z) axis through the atom.
# <7> - "Coriolis force outward (selection 1) and to the axis (selection 2)" : all the restrained atoms get the force propotional to the square of the distance to the central axis. Force will be in the direction from the central (z) axis through the atom
# <8> - "constant shift outward (selection 1) and to the axis (selection 2)" : target coordinate of the atom shifts every time in radial direction by the fixed distance relative to the current coordinate of the atom
# <9> - "restrained center of mass of every subselection" : atoms of every subselection provided as a sublist in the "selection" variable (for one selection use one sublist like {{resname ALA}} ) will be harmonically restrained to tranlsated location such that COM of every subselection will be restrained to it's location in the reference file
# <10> - "restrained center of mass of every fragment in selection" : atoms of every fragment in the "selection" will be harmonically restrained to tranlsated location such that COM of every fragment will be restrained to it's location in the reference file
targetCalculationMode 9
# Mode of scaling of the spring constants :
# <0> - "fixed constant"
# <1> - "exponential increase" .
# <2> - "constant force" mode (constants adjusted such that shift by 1 A gives initially the same amount of energy.
# <3> - "RMSD gradient" mode : spring constant is increased $multiplierConstant times, if relative decrease in RMSD during the last simulation step was smaller, than required value $RmsdGradient (particular case can be RmsdGradient = 0, which maintains the simulation at constant RMSD from symmstric structure); If RMSD decrease was larger, than required $RmsdGradient amount, then spring constant is decreased $multiplierConstant times.
# <4> - "oscillating constant" : spring constant amount will periodically increase and decrease exponentially (linear in log scale) between the $oscillatingConstantMin and $oscillatingConstantMax with the rate of $multiplierConstant/step and $oscillatingConstantPeriod (once in a oscillating period it will go up and down). The first hal-cycle will be decrease of the constant, so initial constants should be at their maximal values. After complete reductin cycle they should not be less than 0.001
# <5> - "linear increase" Coefficient=initialConstant+multiplierConstant*timestep. For "smooth" system should lead to the constant force mode.
# <6> - "parabolic increase" Coefficient=initialConstant+(multiplierConstant*timestep)^2. For "smooth" system should lead to the constant energy per A shift mode.
# <7> - "square-hyperbolic increase" Coefficient=initialConstant/(1-multiplierConstant*timestep)^2. For "smooth" system should lead to the linear RMSD decrease mode. multiplierConstant*timestep should be < 1. multiplierConstant = (1-initialConstant/maxconstant)/timesteps
constantsScaleMode 7
# Initial value of harmonic spring constant
initialConstant 0.08
#initialConstant 1
# This is the multiplier for exponential growth/decay of the spring constant. "" or {} - Autocalculate the constant
# multiplierConstant 0.01
multiplierConstant {}
# multiplierConstant (1-0.01/10000)/100=0.01
# Amount of energy per one angstrom for "constant force" coefficient mode
energySlopeConstant 1.0
# Target ratio of new RMSD to previous RMSD (for constantsScaleMode 3 "RmsdGradient" method of constant scale mode)
RmsdGradient 1.1
# Minimal value of spring constant for "oscillating constant" spring change mode
oscillatingConstantMin 0.01
# Maximal value of spring constant for "oscillating constant" spring change mode
oscillatingConstantMax 10
# Oscillation period (in steps) of spring constant for "oscillating constant" spring change mode.
oscillatingConstantPeriod 20
# Maximal acceptable target value of RMSD from the average structure. If this value (or lower) was reached, simulation stops
# targetRmsd 0.05
targetRmsd 0.0
# Maximal possible number of parametrization steps, before it stops (if was not stopped earlier by other criterion).
# parametrizationStepsMax 1000
parametrizationStepsMax 100
# Option to keep log (numbered copies) of all output files - parametrized structure, constants file, status file
logOutputFiles 1
# Format to keep log of structure-format output files (target coordinates and spring constants)
logOutputFormat namdbin
# ___ Optional parameters for different target calculation modes. Only parameters for the used mode are required
# Target Cylinder radius for "cylindrical projection target" calculation mode
cylinderRadius 45
# Shift per parametrizatin step for "constant shift" mode : target coordinate of the atom shifts every time in radial direction by the fixed distance relative to the current coordinate of the atom
constantShift 0.5
# Twist (in degrees) for the direction of force for different restrain modes. Positive direction is counterclockwise looking from the top of z axis
twist 0
# Twist (in degrees) for the direction of force for different restrain modes. Positive direction is counterclockwise looking from the top of z axis. Parameter for the selection2 for complex restraints
twist2 0
#