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

[Phil Dude]

Hi Tsjerk,

I tried a number of things, including producing a reduced .xtc (which
just the atoms in ), and the match .tpr. I tried fitting too. Nothing
seemed to work, and strangely, it seemed that it failed on multi frame.
When I gave it junk (not C-alpha's just normal group), it happily
produced loads of output, before terminating.

So what worked was writing a .pdb with *just* the C-alphas and the
matching .tpr file, and then when asked for index group you can give "0
0" and I get output.

I suspect, there's something subtle here...

On my second point, the .xvg files don't work in xmgrace, or any other
tool. It seems to be written as "$frame 0 <Num-Calpha-atoms data>" with
one frame per line. I think that's going to be a 3D plot, so perhaps
needs another tool...?


P.

On 06/18/2016 03:51 AM, Tsjerk Wassenaar wrote:
> 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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> 
> 
>