[gmx-users] g_velacc problem
dommert at icp.uni-stuttgart.de
Wed Oct 13 09:20:11 CEST 2010
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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.
> 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?
> 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
Institute for Computational Physics
EMail: dommert at icp.uni-stuttgart.de
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