Handy Routines for Ptraj in AMBER 9 and AmberTools 1.x

I have extended the functionality of the AMBER9/AmberTools 1.x ptraj utility to include a few things that I need for my own work:

  1. a mostly rewritten diffusion code
  2. mean residence time calculations based on a) the survival function and b) the "standard" autocorrelation function [1-3]. (alternative method described in selected reponses from the Amber mail reflector)
  3. a simple routine to calculate distances to nearest neighbour boxes

For the moment I only put three files here: actions.c containing the three routines (transformDiffusion: diffusion code, transformMRT: mean residence times, transformImgDist: distances to neighbour images; helper functions calculateMSD and increaseMem), the header file actions.h (this is for AmberTools 1.x, older unsupported files for AMBER 9: old9_actions.c and old9_actions.h) and the version.h (version information). Further modifications to the ptraj source code is necessary to make things work, i.e. files ptraj.c and dispatch.c need to be changed. Please be aware that there might still be bugs, so check results carefully!

If there is sufficient interest I will put more info here in the future. Feel free to contact me by email hannes(_a.t_)this_domain.

References:

  1. R. W. Impey, P. A. Madden and I. R. McDonald, J. Phys. Chem. 87(1983), 5071.
  2. A. E. Garcia and L. Stiller, J. Comput. Chem. 14(1993), 1396.
  3. C. Schröder, T. Rudas, S. Boresch, O. Steinhauser, J. Chem. Phys. 124(2006), 234907.
Hannes Löffler

Last modified: Thu Jul 3 13:18:40 BST 2008