-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 10/13/2010 01:01 PM, Eudes Fileti wrote: > Hi Florian, thank you for your help! > I informed at the file.mdp that the velocities should be saved: > > ; OUTPUT CONTROL OPTIONS > ; Output frequency for coords (x), velocities (v) and forces (f) > nstxout = 10 > nstvout = 10 > nstfout = 0 > ;
Hi, I took a quick look at the code and realized that the problem is the -m flag. I will try to fix this and report ASAP. /Flo > > Also, I checked the trajectory using gmxcheck and I got this: > > Checking file traj.trr > trn version: GMX_trn_file (single precision) > Reading frame 0 time 0.000 > # Atoms 7178 > Last frame 150000 time 3000.000 > > > Item #frames Timestep (ps) > Step 150001 0.02 > Time 150001 0.02 > Lambda 150001 0.02 > Coords 150001 0.02 > Velocities 150001 0.02 > Forces 0 > Box 150001 0.02 > > > So I believe that velocities are OK. > I've been using version 4.5 and not version 4.5.1, > Do you believe that's the problem? Or it could be memory problem? > _______________________________________ > 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 > > > > 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: [email protected] > <mailto:[email protected]> > Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert > > > - -- 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: [email protected] 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/ iEYEARECAAYFAky1oTwACgkQLpNNBb9GiPkjAQCgvNhU0sIA+SDpDHo2cRSWhgNH C5oAmwZRn7UZoJ0HSjXhIvwU1D50UIpt =fjov -----END PGP SIGNATURE----- -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
