<div>Hi Florian, thank you for your help!</div><div>I informed at the file.mdp that the velocities should be saved:</div><div><br></div><div>; OUTPUT CONTROL OPTIONS</div><div>; Output frequency for coords (x), velocities (v) and forces (f)</div>
<div>nstxout = 10</div><div>nstvout = 10</div><div>nstfout = 0</div><div>;</div><div> </div><div>Also, I checked the trajectory using gmxcheck and I got this:</div><div><br>
</div><div>Checking file traj.trr</div><div>trn version: GMX_trn_file (single precision)</div><div>Reading frame 0 time 0.000 </div><div># Atoms 7178</div><div>Last frame 150000 time 3000.000 </div><div>
<br></div><div><br></div><div>Item #frames Timestep (ps)</div><div>Step 150001 0.02</div><div>Time 150001 0.02</div><div>Lambda 150001 0.02</div><div>Coords 150001 0.02</div><div>
Velocities 150001 0.02</div><div>Forces 0</div><div>Box 150001 0.02</div><div><br></div><div><br></div><div>So I believe that velocities are OK.</div><div>I've been using version 4.5 and not version 4.5.1, </div>
<div>Do you believe that's the problem? Or it could be memory problem? </div>_______________________________________<br>Eudes Eterno Fileti<br>Centro de Ciências Naturais e Humanas<br>Universidade Federal do ABC — CCNH<br>
Av. dos Estados, 5001<br>Santo André - SP - Brasil<br>CEP 09210-971<br><a href="http://fileti.ufabc.edu.br" target="_blank">http://fileti.ufabc.edu.br</a><br>
<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
On 10/12/2010 11:12 PM, Eudes Fileti wrote:<br>
> Hi everybody, I'm trying to use g_velacc to calculate the diffusion<br>
> coeficient for my solute.<br>
> For this, I performed a simple simulation to test such tool.<br>
><br>
> 1000 water molecules,<br>
> NPT ensemble<br>
> positions and velocities colected every 0.01ps<br>
> Gromacs 4.5.<br>
><br>
> However, once I run: g_velacc -f traj -s -n index.ndx -o -m -acflen<br>
> 1000 -nonormalize<br>
><br>
> I get the following error:<br>
><br>
> Group 0 ( System) has 3000 elements<br>
> Group 1 ( SOL) has 3000 elements<br>
> Group 2 ( OW) has 1000 elements<br>
> Group 3 ( HW1) has 1000 elements<br>
> Group 4 ( HW2) has 1000 elements<br>
> Select a group: 1<br>
> Selected 1: 'SOL'<br>
> trn version: GMX_trn_file (single precision)<br>
> Reading frame 0 time 0.000 Segmentation fault<br>
<br>
Recently I used g_velacc in gmx 4.0.7 and it worked fine. Now I just<br>
tested the gmx4.5.1 version for you and it also worked. So it seems that<br>
there is something wrong with your trajectory. Are you sure that<br>
velocities were saved, which is not the case for an xtc file. You have<br>
to explicitly define nstvout in your mdp file, that tells gromacs how<br>
often the velocities should be written to the trr file.<br>
<br>
/Flo<br>
<br>
><br>
> I've tried several things. I changed flag values. I tried the -mol<br>
> option. I tried converting a trajectory<br>
> to another format (.trj). I tried using the version 3.3.3 of g_velacc.<br>
> Nothing worked, always the same error.<br>
> Could someone give me a hand?<br>
> Grateful<br>
> eef<br>
> _______________________________________<br>
> Eudes Eterno Fileti<br>
> Centro de Ciências Naturais e Humanas<br>
> Universidade Federal do ABC — CCNH<br>
> Av. dos Estados, 5001<br>
> Santo André - SP - Brasil<br>
> CEP 09210-971<br>
> <a href="http://fileti.ufabc.edu.br" target="_blank">http://fileti.ufabc.edu.br</a><br>
><br>
<br>
<br>
- --<br>
Florian Dommert<br>
Dipl.-Phys.<br>
<br>
Institute for Computational Physics<br>
<br>
University Stuttgart<br>
<br>
Pfaffenwaldring 27<br>
70569 Stuttgart<br>
<br>
Phone: +49(0)711/685-6-3613<br>
Fax: +49-(0)711/685-6-3658<br>
<br>
EMail: <a href="mailto:dommert@icp.uni-stuttgart.de">dommert@icp.uni-stuttgart.de</a><br>
Home: <a href="http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert" target="_blank">http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert</a></blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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