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 <phild...@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 > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.