On Wed, Dec 21, 2011 at 18:44, SebastianWaltz <[email protected]> wrote: > Hi all, > > I try to reproduce the results from g_angle using my own c++ code. Using > the formula > > θ=acos(r_ij * r_kj/|r_ij||r_kj|) > > with the acos from the cmath library, I obtain an angle which is always > ~5% larger when the angel calculated by g_angle. > Does g_angle use the same formula or does it calculate θ in a different way?
The angles are calculated through src/gmxlib/bondfree.c::bond_angle() which does (after taking care of PBC): *costh=cos_angle(r_ij,r_kj); th=acos(*costh); cos_angle() is defined in include/vec.h to do r_ij * r_kj/|r_ij||r_kj|; acos() comes from the math lib, it's not a GROMACS function. So it's essentially what you seem to do. I guess approximations and precision loss might play a role, f.e. cos_angle() uses GROMACS' own gmx_invsqrt() - do you use math lib sqrt() to calculate the vector norm ? You could try cut-and-pasting the few pieces of code making up the GROMACS implementation of these functions - they are well contained in include/vec.h. Cheers, Bogdan -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
