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

[Tsjerk Wassenaar]

Hi Phil,

Did you write all atoms to the trajectory or only a group? Does the
reference structure match the trajectory? The Jacobi error usually occurs
when there is a mismatch, and the route via a PDB file is consistent with
that.

Cheers,

Tsjerk

On Sat, Jun 18, 2016 at 3:25 AM, Phil Dude <phildude at earthlink.net> wrote:

> 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
> >
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-- 
Tsjerk A. Wassenaar, Ph.D.