Hello Could you please clarify what is the reason for adopting the "all-bonds" constraints as a standard practice in gmx protein simulations?
I mean, the argument that "the time step in molecular simulations can be increased by a factor of 4 by replacing the bond vibrations by holonomic constraints' (LINCS paper) seems valid to me in the case of bonds that contain hydrogen (10 fs vibration period for a C-H bond). Why there is a need (if any) to turn ALL bonds to constraints? Furthermore, has anybody seen a difference in the ps/ns protein dynamics when switching from all-bonds to h-bonds constraints? My opinion is that if bond vibrations take place in the fs timescale AND are uncoupled to the slower degrees of freedom , the choice of constraints shouldn't matter, apart from the computation cost of course. I would really appreciate any comments on these issues. Many thanks in advance. George Patargias -- 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
