[gmx-users] g_tcaf segmentation fault

[Stelios Karozis]

I check my .mdp setting and you were right. I haven't been saving the 
velocities in my .trr file. I change my setting and everything worked fine.

Thanks for your help

Stelios

On 09/27/2012 03:37 PM, Tsjerk Wassenaar wrote:
> Re: [gmx-users] g_tcaf segmentation fault
>
> The .trr file can contain coordinates, velocities, and forces over
> time, depending on your .mdp settings (nstxout, nstvout, nstfout). For
> g_tcaf, you need to have velocities. It does say so in the manpage.
> Run gmxcheck to see what's in your .trr file.
>
> A segmentation fault with the analysis tools is usually an indication
> that there is a mismatch in data, e.g. between trajectory and
> reference structure, or that some data is missing, like velocities in
> a trajectory. Of course the developers could try and catch all those
> things, but they rather spend their time thinking of new things :p
>
> Cheers,
>
> Tsjerk
>
> On Thu, Sep 27, 2012 at 2:18 PM, Stelios Karozis
> <skarozis at ipta.demokritos.gr> wrote:
> > Sorry, but i was wrong, the .trr file contains trajectories and the .gro
> > output file contains velocities as it should.
> >
> > Stelios
> >
> >
> > On 09/27/2012 03:03 PM, Stelios Karozis wrote:
> >>
> >> Hi Tsjerk,
> >> I checked my .trr file and it contains the velocities, as it should.
> >>
> >> Stelios
> >> On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote:
> >>>
> >>> Hi Stelios,
> >>>
> >>> Does your .trr file contain velocities?
> >>>
> >>> Cheers,
> >>>
> >>> Tsjerk
> >>>
> >>> On Sep 26, 2012 8:24 PM, "Stelios Karozis" 
> <skarozis at ipta.demokritos.gr>
> >>> wrote:
> >>>
> >>> Thanks for the response. First i tried the .trr from the 
> simulation and
> >>> the
> >>> result was segmentation fault.
> >>> I use g_covar for entropy estimation combined with g_anaeig 
> command. So
> >>> the
> >>> use of g_covar .trr file as an input, was easy alternative .trr 
> file to
> >>> see
> >>> if i will get pass the segmantation fault error. I didn t give it too
> >>> much
> >>> thought.
> >>>
> >>> Stelios
> >>>
> >>> Ο χρήστης Justin Lemkul <jalemkul at vt.edu> έγραψε:
> >>>
> >>> On 9/26/12 12:55 PM, Stelios Karozis wrote: > Thanks for the 
> suggestion.
> >>> >
> >>> I just tried and the p...
> >>>
> >>> The trajectory written from g_covar contains eigenvectors from PCA. I
> >>> don't
> >>> understand why you wou...
> >>>
> >>> -- ======================================== Justin A. Lemkul, Ph.D.
> >>> Research Scientist Department ...
> >>
> >>
> >
> > --
> > ------------------
> > Stelios Karozis
> > Research Assistant
> > Environmental Research Lab
> > IN-RAS-TES - NCSR Demokritos - Greece
> > email: skarozis at ipta.demokritos.gr
> > tel  : 0030 210 650 3403
> >
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada
> --
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-- 
------------------
Stelios Karozis
Research Assistant
Environmental Research Lab
IN-RAS-TES - NCSR Demokritos - Greece
email: skarozis at ipta.demokritos.gr
tel  : 0030 210 650 3403