[gmx-users] mdrun: broken molecules?

[David van der Spoel]

Perttu Niemelä wrote:
> Dear David,
> 
> I am quite sure of both. To describe the situation more
> clearly, I copy-pasted below the coordinates of one
> molecule at a few stages of the simulation. In each
> case, after converting to gro, I checked with gmxdump that
> these are exactly the coordinates in .tpr and .xtc files.
> 
> How does mdrun decide on which atoms should be kept
> together? Perhaps I am missing something obvious here?
> 
> 1) Initial configuration (from .tpr)
> ====================================
>   127DPPC   NC3 1513   4.939   0.585   6.960
>   127DPPC   PO4 1514   4.565   0.271   6.959
>   127DPPC   GL1 1515   4.456   0.318   6.508
>   127DPPC   GL2 1516   4.106   0.404   6.414
>   127DPPC   C1A 1517   4.379   0.296   6.060
>   127DPPC   C2A 1518   4.469   0.468   5.752
>   127DPPC   C3A 1519   4.771   0.477   5.404
>   127DPPC   C4A 1520   4.983   0.731   5.051
>   127DPPC   C1B 1521   3.928   0.449   5.934
>   127DPPC   C2B 1522   4.024   0.485   5.487
>   127DPPC   C3B 1523   4.341   0.499   5.190
>   127DPPC   C4B 1524   4.535   0.629   4.899
> 
> 2) At timeframe N (from .xtc)
> =============================
>   127DPPC   NC3 1513   4.099   0.003   6.747
>   127DPPC   PO4 1514   4.011   0.320   6.473
>   127DPPC   GL1 1515   4.341   0.200   6.056
>   127DPPC   GL2 1516   4.136   0.434   5.918
>   127DPPC   C1A 1517   4.584   0.090   5.635
>   127DPPC   C2A 1518   4.554   0.154   5.241
>   127DPPC   C3A 1519   4.530   0.190   4.756
>   127DPPC   C4A 1520   4.611   0.251   4.352
>   127DPPC   C1B 1521   4.073   0.173   5.607
>   127DPPC   C2B 1522   3.945  -0.074   5.247
>   127DPPC   C3B 1523   3.865  -0.358   4.900
>   127DPPC   C4B 1524   3.613  -0.389   4.521
> 
> 3) At timeframe N+1 (see y-coordinate)
> ======================================
>   127DPPC   NC3 1513   3.936   6.210   7.009
>   127DPPC   PO4 1514   4.060   6.450   6.650
>   127DPPC   GL1 1515   4.123   6.550   6.164
>   127DPPC   GL2 1516   4.312   6.845   6.172
>   127DPPC   C1A 1517   4.130   6.532   5.584
>   127DPPC   C2A 1518   4.305   6.438   5.189
>   127DPPC   C3A 1519   4.598   0.194   4.846
>   127DPPC   C4A 1520   4.956   0.019   4.513
>   127DPPC   C1B 1521   4.045   0.707   5.823
>   127DPPC   C2B 1522   3.893   0.673   5.363
>   127DPPC   C3B 1523   3.833   0.417   5.130
>   127DPPC   C4B 1524   3.793  -0.035   5.205
> 
> Regards,
> Perttu
> 
> On Wed, 22 Nov 2006, David van der Spoel wrote:
> 
>> Perttu Niemelä wrote:
>>> Dear gmx-users,
>>>
>>> Is it true that mdrun (3.3.1) should not write broken
>>> molecules under any circumstances? If the .xtc output
>>> contains broken molecules, should one be worried?
>>>
>>> The molecules in my .xtc file are whole for the most of the
>>> time, but at some frames one or two are broken such that parts
>>> of the molecule are on opposite sides of the periodic box. I
>>> checked this with gmxdump and a short code of my own. Also,
>>> I was not able to make the molecules whole again with any of
>>> the -pbc options in trjconv. The molecules in the initial
>>> configuration are whole and I cannot see any reason for this.
>>>
>>> Best Regards,
>>>
>>> Perttu Niemela
>>> Helsinki Univ. Tech.
>>> Finland
>
Weird.

Please submit a bugzilla starting as close to timeframe N as possible.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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