[gmx-users] Biasing a dipole vector direction relative to the moment of inertia tensor eigenvectors

Andrew Ritchie drew.w.ritchie at gmail.com
Thu Apr 26 19:58:20 CEST 2012


I am trying to do electrostatics calculations for a protein system which requires knowledge of the average dipole vector for an experimental probe.  I've previously obtained this average dipole vector by using umbrella sampling with WHAM over the chi_2 dihedral angle of this probe, however, it's become clear that the chi_1 orientations are important enough to the average dipole vector that being in a local min for chi_1 and biasing the single degree of freedom is not sufficient.  Rather than doing the simulations for 2 DOF, it was suggested that I bias the dipole vector direction relative to the moment of inertia tensor's eigenvectors.  Gromacs has a function for orientation restraints relative to the rotation matrix for each frame, however, this is presented in the context of NMR spectroscopy and observables.  Would it be possible to use the orientation restraints function for umbrella sampling of dipole vector space and is there a straightforward way to interpret the biasing orientation region (which I believe is referred to as the observable in the  manual) as spherical polar coordinates phi and psi?

Andrew Ritchie
The University of Texas at Austin

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