[gmx-users] Re: tpr without top-file

Pim Schravendijk schraven at mpip-mainz.mpg.de
Mon Oct 4 12:08:09 CEST 2004

Try with the 

pbc = no


That is, if your trajectory is actually run without periodic boundaries, 
I guess. But if your run did use periodic boundaries, you must have a box 
size as well, and you shouldn't have to use arbitrary box sizes. Is your 
other program using other units than gromacs (something else than nm)?

Pim Schravendijk - PhD Student
Max Planck Institute for Polymer Research

> From: Peter Zoon <zoon at science.uva.nl>
> Subject: Re: [gmx-users] tpr without top-file
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <41611E6E.1090302 at science.uva.nl>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> I've succesfully made a topology with x2top, but I'm still not able to 
> get a tpr file from this topfile.
> While running grompp a get a lot of warnings like this:
>       WARNING 385 [file "output.top", line 1205]:
>       No default Angle types, using zeroes
> When I ignore the warnings finally grompp crashes on
> ERROR: One of the box vectors is shorter than twice the cut-off length. 
> Increase the box size or decrease rcoulomb.
> But increasing the box size (I started from a pdb, which has no box 
> size? later converted to gro) or decreasing the rcoulomb in the mdp 
> doesn't seem to have any effect.
> Any suggestions apart from the ones already mentioned?
> Peter

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