[gmx-developers] CVS 200800503: grompp hangs when using distance constrained pulling

[Martin Hoefling]

Hi all,

any ideas what is wrong here?

I am trying to COM-seperate constrain two chains. If I generate a run
input, grompp hangs with:

-------------
...
Checking consistency between energy and charge groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 88x88x88, spacing 0.117 0.117 0.117
Pull group  natoms  pbc atom  distance at start     reference at t=0
       0      1726       863
       1      1430      2441
-------------                 ^-Cursor

Pull section in my run input looks like this:

-------------
pull                     = constraint
pull_geometry            = distance
pull_dim                 = Y Y Y
pull_constr_tol          = 1e-06
pull_start               = yes
pull_nstxout             = 10
pull_nstfout             = 1
pull_ngroups             = 1
pull_group0              = chA
pull_weights0            =
pull_pbcatom0            = 0
pull_group1              = chB
pull_weights1            =
pull_pbcatom1            = 0
pull_vec1                = 0.0 0.0 0.0
pull_init1               = 0.0
pull_rate1               = 0
pull_k1                  = 0

-------------

I've uploaded a tarball with all necessary files to reproduce it
(hopefully). This happens for some, but not all of my (equilibrated and
positionrestrained-relaxed) simulations.

http://www.cip.physik.uni-muenchen.de/~Martin.Hoefling/gromacs/grompp-hang.tar.gz

Best wishes
          Martin