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 [[email protected]] HY> Sent: Friday, January 23, 2009 1:14 PM HY> To: He, Yang HY> Cc: [email protected] 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 [[email protected]] HY>> Sent: Friday, January 23, 2009 12:04 PM HY>> To: [email protected] 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? _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
