[gmx-users] mdrun: broken molecules?

[David van der Spoel]

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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