Hi all, I am trying to do an umbrella sampling of a fairly extended state of the protein along end-to-end distance of it. I am using a rectangular box ( elongated along x ) of dimension 20 nm X 8nm X 8 nm. I am doing the simulation in NVT ensemble. gromacs 4.5.4 is being used.
But, even after running for 1 ns, the simulation crashes saying that Program mdrun_5mpi, VERSION 4.5.4 Source code file: pull.c, line: 329 Fatal error: Distance of pull group 1 (2.940209 nm) is larger than 0.49 times the box size (9.000000) But if I see the trajectory, it hardly shows any issue with seeing the PBC image . I am not sure how to avoid this issue. Should I make one of the endgroup as freeze group so that it does not get tilted. Any help will be appreciated. Sanku -- 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
