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

[Eudes Fileti]

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


>
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