Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought.
Stelios Ο χρήστης Justin Lemkul <jalem...@vt.edu> έγραψε: 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 ======================================== -- 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
