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<br><br>> Date: Mon, 21 Sep 2009 09:11:24 +0200<br>> From: anna.marabotti@isa.cnr.it<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Re: Re: problems running REMD on grids<br>> <br>> Dear Mark,<br>> <br>> I passed your suggestion to omit the -s flag to the person who developed the<br>> scripts to launch GROMACS on the grid (I'm only a final user with no<br>> permission to modify the scripts). We made several trials and I don't know<br>> exactly all the modifications he applied during all trials (it's not exactly<br>> a script that I launch as an .exe file, the system is a bit more complex and<br>> I cannot see directly the commands). In the final version of the script I<br>> know that the flag -s was kept with the suggestion of adding only the name<br>> of the tpr files, without extension. Now it works.<br>> <br>> Anna<br>> <br>> <br>> Date: Sat, 19 Sep 2009 05:22:16 +1000<br>> From: Mark Abraham <Mark.Abraham@anu.edu.au><br>> Subject: Re: [gmx-users] Re: problems running REMD on grids<br>> To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> Message-ID: <4AB3DDE8.8000201@anu.edu.au><br>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>> <br>> Anna Marabotti wrote:<br>> > Dear gmx-users,<br>> > after a lot of trial (and errors) I finally got my REMD simulation. The<br>> > problem was solved essentially when we avoided indicating the extension of<br>> > the .tpr files: i.e.<br>> > <br>> > mdrun -s REMD_.tpr -multi 16 -replex 1000 -deffnm REMD_ -np 16<br>> > did not work, whereas<br>> > <br>> > mdrun -s REMD_ -multi 16 -replex 1000 -deffnm REMD_ -np 16<br>> > did work.<br>><br><br>This is very strange.<br>Both command lines work fine for me.<br>BTW: note that mdrun has no option -np.<br><br>Berk<br> <br>> This sounds tantamount to my suggested solution of omitting the -s <br>> parameter entirely. Did you try that? Did it work?<br>> <br>> > I'm posting it to leave a trace in the gmx-users archive; I'd suggest to<br>> > correct accordingly the example in the part "Execution steps" at<br>> > http://oldwiki.gromacs.org/index.php/REMD<br>> <br>> Dallas Warren wrote that originally, but I'll update it if you'll <br>> confirm the above.<br>> <br>> Mark<br>> <br>> <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>                                            <br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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