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