[gmx-users] problem with pull code

Sanku M msanku65 at yahoo.com
Sat Oct 13 21:17:48 CEST 2012

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.

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