[gmx-users] SOLVED: Re: helixorient, jacobi iteration or junk output...?

[Phil Dude]

Hi,

OK after some messing around, it appears the bug is in the use of.xtc as
input.


I dumped the C-alpha atoms as a .pdb (using trjconv) and then the .ndx
selection is "0 0". Seems to complete without crashing or the jacobi error.

Now, we need to fix the .xvg format to be something useful. Everyone
reporting they just get a line, is the format being slightly off, and
the data being perhaps more complex than is easy to import without some
work?

Cheers

P.

On 06/17/2016 05:58 PM, Phil Dude wrote:
> Hi,
> 
> I am trying to use helixorient to analyse my trajectories, using gromacs
> 5.0.2
> 
> It appears to fail on:
> 
> Program gmx, VERSION 5.0.2
> Source code file:
> /build/gromacs-dDhxvD/gromacs-5.0.2/src/gromacs/linearalgebra/nrjac.c,
> line: 163
> 
> 
> If I allow it to process more than one frame. I have tried to reduce my
> data set and index files to contain SOLEY a single helix and the index
> file just the C-alpha atoms.
> 
> Is this tool in active development?
> 
> Is there specific way in which the tool is supposed to be used?
> 
> I seem to have run out of ideas!
> 
> Regards
> 
> PHiL
>