[gmx-users] mdrun: broken molecules?

[Perttu Niemelä]

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
> > _______________________________________________
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> Are you sure that this is a single molecule *and* that the molecule was
> not broken in the input?
>
> --
> 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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