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

[Berk Hess]

Hi,

This was a stupid and nasty bug in the pbc CVS code.
It only happended when distances were requested for atom pairs
that were separated by large distances in triclinic boxes.
I have fixed it.

Thanks for reporting this,

Berk.

Martin Hoefling wrote:
> 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
>
>
>
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