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