Dear gmx-users, I have some questions on the way that gromacs remove the rotation around the center of mass when set "comm-mode = Angular”
I have checked the related code for removing the rotation and have a question on how gromacs estimate the inertia tensor I. In gromacs, the inertia tensor is estimated as follows, I=sum m_i*[x_i*x_i]-M*[x_c*x_c] here, m_i is the mass of atom i; x_i is the Cartesian coordinate of atom i; x_c is the center of mass; M is the total mass of the system. [x*x] represents the outer product between x and x. One can easily get that I=sum m_i*[y_i*y_i] with y_i = x_i - x_c ———(1) However, from standard mechanics textbook, the inertia is given as I=sum m_i*{(y_i.y_i)E - [y_i*y_i]} ———— (2) here, y_i.y_i is the inner product between y_i and y_i; E is a 3*3 identity matrix. I want to know the reason that gromacs use Eq. (1) instead of Eq. (2) to calculate the inertia tensor. Since gromacs estimate the angular velocity (w) with w=I^-1*L Here, I^-1 is the inverse of the inertia tensor I; L is the angular momentum. The angular velocity will be different using Eq. (1) comparing to Eq. (2) Does anyone know why gromacs use Eq. (1) not Eq. (2)? Thanks, Wenjin -- 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.