in my real application, im trying to calculate the PMF using umbrella sampling along rmsd of the alpha-carbons between two conformations of an enzyme solvated in various calcium concentrations.
since the systems generated by charmmgui are too large to attach, i made a minimal (non-working) example using similar rhodo benchmark (protein, charmm, pppm, npt).
# colvars-rhodo.in
shell cd ../lammps-alphataubio/bench
include in.rhodo
shell cd ../../colvars-rhodo
fix 3 all colvars colvars-rhodo.colvars output colvars-rhodo seed 12345 tstat 2
run 100
# colvars-rhodo.colvars
atoms {
name foo
atomNumbersRange 1-3
}
colvar {
name quux
rmsd {
# atoms { atomsOfGroup foo }
atoms { atomNumbersRange 1-3 }
refPositions { (-6.80572,-9.10264,-32.2296) (-6.81746,-9.4978,-33.1915) (-5.86092,-9.04028,-31.7994) }
}
}
harmonic {
colvars quux
centers 0
targetCenters 10
targetNumStages 9
targetNumSteps 10
targetEquilSteps 9
outputFreq 1
outputCenters on
outputEnergy on
writeTIPMF on
}
“Description: This parameter defines a unique name for this atom group, which can be referred to in the definition of other atom groups (including in other colvars) by invoking atomsOfGroup as a selection keyword.”
First, i cant figure out how to use atomsOfGroup to define a group of atoms and refer to it later. there’s no example in colvars manual, or lammps examples directory. Nothing in previous matsci posts either.
colvars: # atomsOfGroup = “foo”
colvars: Error: cannot find atom group with name foo.
ERROR on proc 0: Fatal error in the collective variables module.
(src/COLVARS/colvarproxy_lammps.cpp:294)
Last command: run 100
"Keyword targetEquilSteps⟨⟨Number of steps discarded from TI estimate⟩⟩
Context: harmonic
Acceptable values: positive integer
Description: Defines the number of steps within each stage that are considered equilibration and discarded from the restraint free energy derivative estimate reported reported in the output."
Second by “tugging” on a protein in an unphysical manner at each stage of steered MD, i want to do ~90% of equilibration steps per window to let the protein settle into realistic intermediate structures along the way before collecting PMF measurements. However i get “Error: keyword “targetequilsteps” is not supported, or not recognized in this context.” but im using targetequilsteps in the harmonic context as described in colvars manual.
colvars: Initializing a new “harmonic” instance.
colvars: # name = “harmonic1” [default]
colvars: # colvars = { quux }
colvars: # stepZeroData = off [default]
colvars: # outputEnergy = on
colvars: # outputFreq = 1
colvars: # timeStepFactor = 1 [default]
colvars: # writeTISamples = off [default]
colvars: # writeTIPMF = on
colvars: # centers = { 0 }
colvars: # targetCenters = { 10 }
colvars: # targetNumSteps = 10
colvars: # targetNumStages = 9
colvars: # outputAccumulatedWork = off [default]
colvars: # outputCenters = on
colvars: # forceConstant = 1 [default]
colvars: # decoupling = off [default]
colvars: # targetForceConstant = -1 [default]
colvars: The force constant for colvar “quux” will be rescaled to 1 according to the specified width (1).
colvars: Error: keyword “targetequilsteps” is not supported, or not recognized in this context.
ERROR on proc 0: Fatal error in the collective variables module.
(src/COLVARS/colvarproxy_lammps.cpp:294)
Last command: run 100
$ lmp_beluga -h
Large-scale Atomic/Molecular Massively Parallel Simulator - 7 Feb 2024 - Development
Git info (develop / patch_7Feb2024_update1-366-g069919ddcd)
OS: Linux "Rocky Linux 8.9 (Green Obsidian)" 4.18.0-513.24.1.el8_9.x86_64 x86_64
Compiler: GNU C++ 11.3.0 with OpenMP 4.5
C++ standard: C++17
MPI v3.1: Open MPI v4.1.4, package: Open MPI [email protected] Distribution, ident: 4.1.4, repo rev: v4.1.4, May 26, 2022
Accelerator configuration:
KOKKOS package API: CUDA OpenMP Serial
KOKKOS package precision: double
Kokkos library version: 4.3.0
FFT information:
FFT precision = double
FFT engine = mpiFFT
FFT library = KISS
KOKKOS FFT engine = mpiFFT
KOKKOS FFT library = cuFFT
Installed packages:
ASPHERE CG-DNA CG-SPICA COLVARS EXTRA-DUMP KOKKOS KSPACE MC MOLECULE RIGID