[gmx-users] g_tcaf segmentation fault
skarozis at ipta.demokritos.gr
Wed Sep 26 18:55:27 CEST 2012
Thanks for the suggestion.
I just tried and the problem presists.
Just to be clear, the right way is to use the g_covar.trr file, correct?
Ο χρήστης lina <lina.lastname at gmail.com> έγραψε:
On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote:
> 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"
Segmentation fault involves lots.
If I were you, I would try -dt 100 or large to reduce memory
requirement. or perhaps try the very short time period. namely -e 200 to
see what's going on.
> 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
> -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
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