On 9/26/12 12:55 PM, Stelios Karozis wrote:
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?
The trajectory written from g_covar contains eigenvectors from PCA. I don't
understand why you would use that here. Use the trajectory from the actual
simulation.
-Justin
Ο χρήστης lina <lina.lastn...@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.lastn...@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
--
========================================
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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