[gmx-users] Re[4]: why the trajectory file is not output

Vitaly Chaban vvchaban at gmail.com
Fri Jan 23 22:50:49 CET 2009

If your version is not current gromacs users always advise to
upgrade up to the last one.

Did you try to use mdp file from those systems which run correctly?

As for the last error, did it happen when you just reduce the number of
steps? It cannot be so...

I guess you may experience the problems with memory if your system is
very large.

HY> Hi I just use the 3.3.1,not very new version. Also, I have tried
HY> to reduce the number of steps while It does not work. Always, it shows that

HY> starting mdrun 'MODEL CYLINDER'
HY> 10000 steps,    300.0 ps.

HY> Segmentation fault (core dumped)

HY> I am not very sure about that.

HY> Yang
HY> ________________________________________
HY> From: Vitaly Chaban [vvchaban at gmail.com]
HY> Sent: Friday, January 23, 2009 1:14 PM
HY> To: He, Yang
HY> Cc: gmx-users-request at gromacs.org
HY> Subject: Re[2]: why the trajectory file is not output

HY> Try to copy grompp.mdp from the working system and start the run with
HY> the problematic one. At least we will understand where to look for
HY> the bug.

HY> So what is the version of your gromacs, you didn't still answer.

HY>> Hi, As for the version, I can get the trajectory file when I run
HY>> other cases using command"mdrun". In addition, when I run this case, the other
HY>> files like "topol.tpr, ener.edr, mdout.mdp,md.log" can be output expect  the trr or xtc file.

HY>> I am not sure why this happened.

HY>> ________________________________________
HY>> From: Vitaly Chaban [vvchaban at gmail.com]
HY>> Sent: Friday, January 23, 2009 12:04 PM
HY>> To: gmx-users-request at gromacs.org
HY>> Cc: He, Yang
HY>> Subject: Re: why the trajectory file is not output

gurgo>>> When I use the command "mdrun"to simulate the CG DNA model, I found that  all the  files are output expect the trajectory file. I
gurgo>>> will list
gurgo>>> some parts of my mdp.file

HY>> What about another systems? Do they output the trajectory? What
HY>> version of gromacs do you use by the way? Do you run in parallel?

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