PELE ANM

From Jacobson Lab Wiki

Jump to: navigation, search

Possible parameters

If it necessary to turn on anm moves with anm_freq 1 (or some other integer) to run anm steps

      anm_freq [integer]                  : Set frequency of anm steps (defualt it never)
      anm_altm_type [integer]             : Choose mode and direction in the following ways (default = 3):-
                                          : 1 = Pick the mode and direction used in the last ANM step
                                          : 2 = Pick the mode with highest projection to last one
                                          : 3 = Pick a random mode from those calculated and a random direction
                                          : 4 = Toggle the direction in the mode already specified
                                          : 5 = Cycle through the calculated modes and directions +1,-1,+2,-2,+3,-3
                                          : 6 = Pick random modes and pick a direction to move away from native structure
                                          : 7 = Cycle through modes and pick a direction to move away from native structure
                                          : 8 = Cycle through modes and leave picking a direction to something else
                                          : 9 = Pick random modes and leave picking a direction to something else
                                          : 10 = Same as 3 except choice of mode is biased by the eigenvalue
                                          : 11 = pick a random mode (1-neig) and a new direction +/- also modes with
                                          :     lower freq are more probable (by eigenvalue ranking)
                                          : 12 = Same as 10 except direction is left for something else
                                          : 13 = Same as 10 except direction is picked to move away from the native
                                          : 14 = Do nothing
      anm_altm_freq [integer]             : Change mode, direction and/or movement vectors with this frequency (default = 1)
      anm_eig_freq [integer]              : Frequency with which to calculate fresh eigenmodes (default = 1)
      anm_prs [yes/NO]                    : Use the PRS ANM sampling method..
                                          : In this implimentation the of Perturbation response methodmatrix K is removed
                                          : and any parts of the system outside of the cutoff is not included in the computation.
                                          : Ref:Ikeguchi,M., et al. Physical Review letters 94:078102, 2005
      anmsamp [YES/no]                    : Use ANM method where all HAs (heavy atoms) are displaced down eigenvectors
                                          : and no springs are used.  The energy of the new atom positions is tested to see
                                          : if it is below the old energy scaled by the parameter oldscale if not the move is
                                          : tried again using different modes. An optional minimisation can be carried out after th
                                          : if it is below the old energy scaled by the parameter oldscale if not the move is
                                          : tried again using different modes. An optional minimisation can be carried out after the
                                          : displacement.  Also a scan of the modes can be carried out using anmscan.  The scan
                                          : also has an optional minimisation.
                                          : All hydrogens are displaced with the same vectors as there connected heavy atoms.
                                          : NB. it is advised to use this option with the HA ANM model
      anmscan [integer]                   : When using the anmsamp method scan through the modes and directions and pick them
                                          : with the following options:-
                                          : 1 = Pick mode at and direction at random (default)
                                          : 2 = Pick mode and dir with energy
                                          : 3 = Pick only direction with energy
                                          : 4 = Pick mode with energy and direction with native overlap (anm_altm_type = 8)
                                          : 5 = Do nanmsamp nested ANM trials for each ANM move
      minanms [0/1/2]                     : When using the anmsamp minimise after every energy test or not.
                                          : 0 = minimise after the move has been chosen (default)
                                          : 1 = minimise after every displacement when in the process of choosing
                                          : 2 = dont do an ANM minimisation at all
      nanmsamp [integer]                  : Number of trials allowed for anmsamp
      oldscale [real, 0-1]                : Scaling of the present energy for the anmsamp reasonable energy test
      caconst [real]                      : CA constraint force constant used in PELE minimisation (default = 0.0)
Personal tools