Dear Gromacs users, Recently I have converted each frame of the trajectory to a pdb file using gromacs tool "g_trjconv" and then have extracted angles from the CRYST1 record of pdb file, to see how they are varying in simulation. By doing so I have observed that my box angles alpha and gamma are not at all varying through out the simulation these values are remains at "90" degrees and there is a change in beta value. I have used "triclinic box" for simulations of my system with angles alpha = 90, beta=120 and gamma=90 and have used "NPT" ensemble with following options in mdp file "pcoupltype = anisotropic and ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 " here my questions are: 1) What might be the probable reason for constant values of alpha and beta ( why these values are not changing). 2) Am I following correct protocol to extract angles, or Is there any better way to extract angles from trajectory. 3) Am I using correct options in .mdp file.
Thank you in advance. Regards, Ramesh. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists