[gmx-developers] CVS 200800503: grompp hangs when using distance constrained pulling
hessb at mpip-mainz.mpg.de
Wed Jun 18 12:34:30 CEST 2008
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,
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.
> Best wishes
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