[gmx-users] g_tcaf segmentation fault

Stelios Karozis skarozis at ipta.demokritos.gr
Wed Sep 26 18:13:11 CEST 2012

The -dt flag is the time step between the frames in ps. I tried the command in any combination i could think of. With -dt without, with -b without, and so on. The only way i get a partial result is to use the .trr file from the simulation and not from the g_covar command and even then i get the density of the system and after that "segmentation fault"

Ο χρήστης lina <lina.lastname at gmail.com> έγραψε:

On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote:
> Dear all,
> I am attempting to calculate the viscosity of a liquid binary system of
> 500 molecules (3050 atoms), via g_tcaf command.
> The system is equilibrated. The list of command I use is:
> /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v
> eigenvec.trr -av average.pdb -l covar.log//
> //g_tcaf -b 0 -e 20000 -dt 0.001 -f eigenvec.trr -s topol.tpr -n
> index.ndx -mol -oc tcaf_cub.xvg  -oa tcaf_all.xvg -o tcaf.xvg -of
> tcaf_fit.xvg/

-dt 0.001 ?

> The result is a Segmentation fault error:
> /Selected 0: 'System'//
> //trn version: GMX_trn_file (single precision)//
> //Last frame         -1 time    0.000/*/
> /**/Segmentation fault/*
> I use GROMACS 4.5.5
> What am I doing wrong?
> Thanks in advance
> Stelios

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