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 ; 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] > Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert >
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