Hi,
I am not sure how to interpret the cos(theta1) around my reference atom. The help printed is not straightforward when comes to set which atoms forms the angle theta1. For instance. "theta_1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3. theta_2: the angle with the normal of the solvent plane, defined by the same three atoms, or, when the option -v23 is set, the angle with the vector between atoms 2 and 3." In case of water (using default Water group), is oxygen the atom 1 and the hydrogens the atoms 2 and 3? Does it follows the index given by .tpr used for analyses? If so, the distribution as a function of distance gives positive and negative values for cos(theta1). Does positive values means that water oxygen is orient towards my reference at that distance? Cheers! -- Marcelo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
