[gmx-users] g_velacc problem

[Florian Dommert]

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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.

/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: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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