[gmx-users] problem with pull code

Christopher Neale chris.neale at mail.utoronto.ca
Sun Oct 14 22:02:45 CEST 2012

Dear Sanku:

I don't think that your setup is a particularly good idea. In addition to the potential for rotational problems
that you mention, note that the pull force is going to be based on the shortest periodic distance between 
your group0 and group1. This can be across PBC in the Cartesian X dimension, and will be in your system unless 
your protein is < 10 nm long.

Also, you're going to have to present more information to get better assistance. Post your pull code parameters
at the very least. Also, you say that your box dimensions are 20x8x8 nm, but your error message indicates a box
dimension of 9 nm.

Finally, that error message doesn't really make a lot of sense:
"Distance of pull group 1 (2.940209 nm) is larger than 0.49 times the box size (9.000000)"
because 2.94 is less than 0.49*9, not greater as the error message states. I'm not sure if this is a gromacs 
error in an if statement or just a typo in the message that is output.

I should add that you can do some of the testing yourself by using vacuum simulations and boxes of 20x8x8
and 20x20x20 and 50x50x50 (turn off PME for these tests and use the sd integrator) to see which ones give you a

Next time, please use a more informative title.


-- original message --

  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.

More information about the gromacs.org_gmx-users mailing list