[gmx-users] Re: Re: g_velacc problem (Florian Dommert)
fileti at ufabc.edu.br
Wed Oct 13 13:01:28 CEST 2010
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
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
> 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?
> > 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
> 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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