On restraining bonds: The atom moves across the basic unit, i.e. it is not recognising that it should bond via periodic_molecule
Error: The charge group starting at atom 2833 moved than the distance allowed by the domain decomposition (1.615483) in direction X In any case (restraining or not all-bonds) when I am doing grompp, I get a warning - WARNING 1 [file LDH21/em.mdp]: The sum of the two largest charge group radii (1.062153) is larger than rlist (1.000000) I decided to take it as a healthy one, as according to http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb this is because of "Molecules are broken across periodic boundaries, which is not a problem in a periodic system. In this case, the sum of the two largest charge groups will correspond to a value of twice the box vector along which the molecule is broken." -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011290.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
