These options enable and control the calculation and application of additional forces that are derived from three-dimensional densities, e.g., from cryo electron-microscopy experiments. (See the reference manual for details)
density-guided-simulation-active
(no) Activate density-guided simulations.
density-guided-simulation-group
(protein) The atoms that are subject to the forces from the density-guided simulation and contribute to the simulated density.
density-guided-simulation-similarity-measure
(inner-product) Similarity measure between the density that is calculated from the atom positions and the reference density.
inner-product
Takes the sum of the product of reference density and simulated density voxel values.
relative-entropy
Uses the negative relative entropy (or Kullback-Leibler divergence) between reference density and simulated density as similarity measure. Negative density values are ignored.
cross-correlation
Uses the Pearson correlation coefficient between reference density and simulated density as similarity measure.
density-guided-simulation-atom-spreading-weight
(unity) Determines the multiplication factor for the Gaussian kernel when spreading atoms on the grid.
unity
Every atom in the density fitting group is assigned the same unit factor.
mass
Atoms contribute to the simulated density proportional to their mass.
charge
Atoms contribute to the simulated density proportional to their charge.
density-guided-simulation-force-constant
(1e+09) [kJ mol-1] The scaling factor for density-guided simulation forces. May also be negative.
density-guided-simulation-gaussian-transform-spreading-width
(0.2) [nm] The Gaussian RMS width for the spread kernel for the simulated density.
density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width
(4) The range after which the gaussian is cut off in multiples of the Gaussian RMS width described above.
density-guided-simulation-reference-density-filename
(reference.mrc) Reference density file name using an absolute path or a path relative to the to the folder from which gmx mdrun is called.
density-guided-simulation-nst
(1) Interval in steps at which the density fitting forces are evaluated and applied. The forces are scaled by this number when applied (See the reference manual for details).
density-guided-simulation-normalize-densities
(true) Normalize the sum of density voxel values to one for the reference density as well as the simulated density.
density-guided-simulation-adaptive-force-scaling
(false) Adapt the force constant to ensure a steady increase in similarity between simulated and reference density.
true
Use adaptive force scaling.
density-guided-simulation-adaptive-force-scaling-time-constant
(4) [ps] Couple force constant to increase in similarity with reference density with this time constant. Larger times result in looser coupling.
density-guided-simulation-shift-vector
(0,0,0) [nm] Add this vector to all atoms in the density-guided-simulation-group before calculating forces and energies for density-guided-simulations. Affects only the density-guided-simulation forces and energies. Corresponds to a shift of the input density in the opposite direction by (-1) * density-guided-simulation-shift-vector.
density-guided-simulation-transformation-matrix
(1,0,0,0,1,0,0,0,1) Multiply all atoms with this matrix in the density-guided-simulation-group before calculating forces and energies for density-guided-simulations. Affects only the density-guided-simulation forces and energies. Corresponds to a transformation of the input density by the inverse of this matrix. The matrix is given in row-major order. This option allows, e.g., rotation of the density-guided atom group around the z-axis by θ degress by using following input: (cosθ,−sinθ,0,sinθ,cosθ,0,0,0,1) .