The .trr file can contain coordinates, velocities, and forces over time, depending on your .mdp settings (nstxout, nstvout, nstfout). For g_tcaf, you need to have velocities. It does say so in the manpage. Run gmxcheck to see what's in your .trr file.
A segmentation fault with the analysis tools is usually an indication that there is a mismatch in data, e.g. between trajectory and reference structure, or that some data is missing, like velocities in a trajectory. Of course the developers could try and catch all those things, but they rather spend their time thinking of new things :p Cheers, Tsjerk On Thu, Sep 27, 2012 at 2:18 PM, Stelios Karozis <skaro...@ipta.demokritos.gr> wrote: > Sorry, but i was wrong, the .trr file contains trajectories and the .gro > output file contains velocities as it should. > > Stelios > > > On 09/27/2012 03:03 PM, Stelios Karozis wrote: >> >> Hi Tsjerk, >> I checked my .trr file and it contains the velocities, as it should. >> >> Stelios >> On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote: >>> >>> Hi Stelios, >>> >>> Does your .trr file contain velocities? >>> >>> Cheers, >>> >>> Tsjerk >>> >>> On Sep 26, 2012 8:24 PM, "Stelios Karozis" <skaro...@ipta.demokritos.gr> >>> wrote: >>> >>> 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 p... >>> >>> The trajectory written from g_covar contains eigenvectors from PCA. I >>> don't >>> understand why you wou... >>> >>> -- ======================================== Justin A. Lemkul, Ph.D. >>> Research Scientist Department ... >> >> > > -- > ------------------ > Stelios Karozis > Research Assistant > Environmental Research Lab > IN-RAS-TES - NCSR Demokritos - Greece > email: skaro...@ipta.demokritos.gr > tel : 0030 210 650 3403 > > -- > 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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
