[gmx-users] What is the meaning of this warning?

David spoel at xray.bmc.uu.se
Tue Jan 6 18:52:01 CET 2004

On Tue, 2004-01-06 at 17:01, Hua Wong wrote:
> I am running a RMSF with a reference .gro structure and a .trr in which I 
> only read the last frame. And I receive the following warning.
> Warning: can not make broken molecules whole without a run input file,
>          don't worry, mdrun doesn't write broken molecules
> Does it mean I have to launch MDRUN on one of the structure? and which 
> one? The .gro reference? or the other one?

no. it means that if your molecule is broken due to pbc, this program
can only fix it when a tpr file is present. normally there is no

> Thanks.
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel

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