-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 10/12/2010 11:12 PM, Eudes Fileti wrote: > Hi everybody, I'm trying to use g_velacc to calculate the diffusion > coeficient for my solute. > For this, I performed a simple simulation to test such tool. > > 1000 water molecules, > NPT ensemble > positions and velocities colected every 0.01ps > Gromacs 4.5. > > However, once I run: g_velacc -f traj -s -n index.ndx -o -m -acflen > 1000 -nonormalize > > I get the following error: > > Group 0 ( System) has 3000 elements > Group 1 ( SOL) has 3000 elements > Group 2 ( OW) has 1000 elements > Group 3 ( HW1) has 1000 elements > Group 4 ( HW2) has 1000 elements > Select a group: 1 > Selected 1: 'SOL' > trn version: GMX_trn_file (single precision) > Reading frame 0 time 0.000 Segmentation fault
Recently I used g_velacc in gmx 4.0.7 and it worked fine. Now I just tested the gmx4.5.1 version for you and it also worked. So it seems that there is something wrong with your trajectory. Are you sure that velocities were saved, which is not the case for an xtc file. You have to explicitly define nstvout in your mdp file, that tells gromacs how often the velocities should be written to the trr file. /Flo > > I've tried several things. I changed flag values. I tried the -mol > option. I tried converting a trajectory > to another format (.trj). I tried using the version 3.3.3 of g_velacc. > Nothing worked, always the same error. > Could someone give me a hand? > Grateful > eef > _______________________________________ > Eudes Eterno Fileti > Centro de Ciências Naturais e Humanas > Universidade Federal do ABC — CCNH > Av. dos Estados, 5001 > Santo André - SP - Brasil > CEP 09210-971 > http://fileti.ufabc.edu.br > - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAky1XaoACgkQLpNNBb9GiPnANQCguXrk56Thb0TmY9qJB+CKNbwH eI0An1FI0cln8dim8/Mp7qLJvE2eysI0 =Yw3G -----END PGP SIGNATURE----- -- 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