[gmx-users] mdrun: broken molecules?

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 22 13:45:34 CET 2006

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 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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