[gmx-users] Re: Re: g_velacc problem (Florian Dommert)

[Florian Dommert]

-----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: dommert at icp.uni-stuttgart.de
>     <mailto:dommert at icp.uni-stuttgart.de>
>     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: dommert at 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/

iEYEARECAAYFAky1oTwACgkQLpNNBb9GiPkjAQCgvNhU0sIA+SDpDHo2cRSWhgNH
C5oAmwZRn7UZoJ0HSjXhIvwU1D50UIpt
=fjov
-----END PGP SIGNATURE-----