[gmx-users] g_tcaf segmentation fault

[Tsjerk Wassenaar]

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