[gmx-users] Can not open file: traj.xtc

[Justin Lemkul]

On 2/17/13 10:11 AM, Sabrina Kemmerer wrote:
> Hi,
>
> the 'ls -lh' output is
>
> -rw-r--r-- 1 sabrina sabrina   32 Feb 11 19:49 c8vectors.ndx
> -rw-rw-r-- 1 sabrina sabrina 7.8M Jan 19 18:54 confout.gro
> -rw-r--r-- 1 sabrina sabrina   33 Feb 11 19:49 labelvektors.ndx
> -rw-r--r-- 1 sabrina sabrina   33 Feb 11 19:49 ligebene.ndx
> -rw-r--r-- 1 sabrina sabrina   24 Feb 11 19:49 tailvec2.ndx
> -rw-r--r-- 1 sabrina sabrina   22 Feb 17 15:20 tailvec.ndx
> -rw-r--r-- 1 sabrina sabrina 3.2M Feb 11 19:48 topol.tpr
> -rw-rw-r-- 1 sabrina sabrina   43 Feb 17 11:27 traj.md5
> -rw-r--r-- 1 sabrina sabrina  21G Feb 11 03:56 traj.xtc
>
> The commands, which I used, were:
> g_rotacf -f traj.xtc -n ligebene.ndx
> g_rotacf -n ligebene.ndx
>
> The exact output part is
>
> Group     0 (          ebene) has     6 elements
> There is one group in the index
> Reading file topol.tpr, VERSION 4.5.4 (single precision)
>
> -------------------------------------------------------
> Program g_rotacf, VERSION 4.5.4
> Source code file:
> /PathToGromacsSource/Gromacs4.5.4-src/gromacs-4.5.4/src/gmxlib/gmxfio.c, line: 519
>
> Can not open file:
> traj.xtc
>
> Thank you for your help!
>

With a file that is 21 GB in size, I suspect all Gromacs programs are going to 
have issues related to memory availability.  What does gmxcheck tell you about 
the file?  Can you use trjconv to produce a short trajectory (just a few frames) 
and run g_rotacf on that shortened trajectory?  If so, the problem is that the 
file is too large to be dealt with.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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