I want to calculate solvent orientation around two types of spherical particle. The solvent has a long alkyl chain. I use sorient with three atoms in the carbon chain in my index group, one at each end and one in the middle. The results are confusing me.
Theta_1 is described as "the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3". Therefore (it seems to me), if the alkyl chain is mostly sticking out perpendicular from the surface of the spherical particle, theta_1 should be close to 0 and cos(theta_1) should be close to 1. If the alkyl chain is more wrapped around the spherical particle, parallel to the surface, theta_1 should be closer to 90 degrees and cos(theta_1) should be closer to 0. However, when I examine the two types of spherical particles visually and compare them to the results from sorient, it seems to be the opposite--the system where the alkyl chain looks (visually) more perpendicular to the particle surface has lower cos(theta_1). Am I misunderstanding which angle exactly theta_1 is or should I just trust the sorient calculation over what appears to me visually? -- 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.