Dear Mark, I passed your suggestion to omit the -s flag to the person who developed the scripts to launch GROMACS on the grid (I'm only a final user with no permission to modify the scripts). We made several trials and I don't know exactly all the modifications he applied during all trials (it's not exactly a script that I launch as an .exe file, the system is a bit more complex and I cannot see directly the commands). In the final version of the script I know that the flag -s was kept with the suggestion of adding only the name of the tpr files, without extension. Now it works.
Anna Date: Sat, 19 Sep 2009 05:22:16 +1000 From: Mark Abraham <mark.abra...@anu.edu.au> Subject: Re: [gmx-users] Re: problems running REMD on grids To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4ab3dde8.8000...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear gmx-users, > after a lot of trial (and errors) I finally got my REMD simulation. The > problem was solved essentially when we avoided indicating the extension of > the .tpr files: i.e. > > mdrun -s REMD_.tpr -multi 16 -replex 1000 -deffnm REMD_ -np 16 > did not work, whereas > > mdrun -s REMD_ -multi 16 -replex 1000 -deffnm REMD_ -np 16 > did work. This sounds tantamount to my suggested solution of omitting the -s parameter entirely. Did you try that? Did it work? > I'm posting it to leave a trace in the gmx-users archive; I'd suggest to > correct accordingly the example in the part "Execution steps" at > http://oldwiki.gromacs.org/index.php/REMD Dallas Warren wrote that originally, but I'll update it if you'll confirm the above. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
