Modified Gromacs Code to Perform Force Covariance Analysis

(Citation: Macromolecular Entropy Can Be Accurately Computed from Force, U. Hensen, Frauke Grater and Richard H. Henchman, J. Chem. Theory. Comput., 2014, 10, 4777).

Instructions:

  • Download the modified gromacs file gmx_covar.4.6.c (version 4.6) or gmx_covar.5.0.4.c (version 5.0.4).
  • Rename the file gmx_covar.c and place it either in the SOURCE/src/tools/ directory (gromacs 4.6.x) or the SOURCE/src/gromacs/gmxana/ directory (gromacs 5.0.x). (you might want to back up the original gmx_covar.c file which does quasiharmonic analysis).
  • Recompile the whole gromacs package as usual as explained in the manual.
  • Make sure a force trajectory is outputted from your simulation.
  • Run gmx_covar using the command g_covar -s STARTFILE.tpr -f TRAJECTORY.trr -mwa -fc (-T TEMPERATURE -n INDEX.ndx)
  • The eigenvalues will be listed in eigenval.xvg in units of J s-2.
  • To see the help text, type g_covar -h .