[gmx-developers] center of mass bug with pulling reference group

Berk Hess hess at cbr.su.se
Tue Apr 27 10:36:23 CEST 2010

Jochen Hub wrote:
>>>> Can you try if that also gives problems?
>>> I have tried, one gets with
>>> pull_geometry            = direction
>>> pull_dim                 = N N Y
>>> pull_vec1                = 0.0 0.0 1.0
>>> pull_init1               = -2.91975
>>> Pull group  natoms  pbc atom  distance at start     reference at t=0
>>>       0      5896      2948
>>>       1         4      5898  -2.326                -2.920           
>>> which is again wrong (and the negative to the "distance" output, as
>>> expected). The correct distance in z-direction is (this time from
>>> g_dist) -2.9742942, not -2.326.
>> Ah, couldn't the problem simply be a pbc issue?
>> What is your z box size?
>> And it your pull pbc reference atom set properly?
> Ah, good point. The box in z-direction is however definitely large
> enough. None of the atoms of the reference group atoms is outside the
> box in z-direction. I have a bilayer well in the middle of the box in
> z-direction.
> However, the pbc atom is sometimes out of the box in x-direction since
> the the initial structure contains non-broken lipids which sometimes
> point out of the box (in the x-y plance). This is definitely the
> problem. When using a pbc_atom in the middle of the bilayer everything
> goes fine. Using a pdb with atoms inside the box does however not
> help, apparently the pull code used non-broken molecule coordinates.
> So we found the issue (thanks for that!), but is that the expected
> behavior? I would expect that, if I only pull in z-direction, a
> pbc_atom out of the box in x-y should not affect the reference
> position. Or am I wrong here?
> Thanks a lot Berk,
> Jochen
In x-y it should not matter.
But what might matter is that distances of atoms in the bilayer to the
pbc atom are larger
than half the box length, if the pbc atom is in a head group instead of
in the middle of the bilayer.


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