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.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 >> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
