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Hi,<br><br>Your command line is incorrect.<br>-reprod should be used without yes.<br>-reprod is yes<br>-noreprod is no<br><br>mdrun -cpi has no effect on your results at all.<br>But always remember that MD is chaotic, there is no point in trying<br>to reproduce trajectories exactly, unless for a very special purpose.<br><br>Berk<br><br>> Date: Thu, 30 Jul 2009 16:53:13 +0200<br>> From: qiaobf@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] question about continuation using tpbconv and mdrun -cpi<br>> <br>> Hi Mark,<br>> <br>> Sorry to trouble you again!<br>> <br>> I made two tests, by using one-processor and one 32-processors on the<br>> same cluster. I used 4000SPC/E waters (OPLS-AA ff.) The former<br>> (one-processor) gives the exactly the same potential. However, the<br>> latter still shown some deviation of the potential. When I use "-reprod<br>> yes", the potential is -190098+-457.199 for "Comparison", and<br>> -190088+-467.225 for "Reference". When I use "-dlb no", -190116+-476.512<br>> for "Comparison", and -190114+-483.749 for "Reference".<br>> <br>> The following is the job script lines when using "-reprod yes":<br>> ********************************************************************************<br>> # Reference<br>> grompp -f full.mdp -c initial.gro -p system.top -o full<br>> mpirun -np 32 mdrun -deffnm full -reprod yes<br>> <br>> # Comparison<br>> grompp -f full.mdp -c initial.gro -p system.top -o full2<br>> mpirun -np 32 mdrun -deffnm full2 -reprod yes -cpt 2 -maxh 0.2<br>> mpirun -np 32 mdrun -deffnm full2 -reprod yes -cpi full2.cpt -append<br>> ********************************************************************************<br>> <br>> Do you have some further ideas?<br>> <br>> best wishes,<br>> Baofu Qiao<br>> <br>> <br>> Mark Abraham wrote:<br>> > Baofu Qiao wrote:<br>> >> Hi Mark,<br>> >><br>> >> Thanks!<br>> >> Because the maximum time for one single job is set to be 24hours on the<br>> >> cluster I'm using, I want to make sure which is the best way to continue<br>> >> the gmx jobs. I wonder how strong effect "mdrun -cpi" has? From the<br>> >> introduction of mdrun, it seems that there are some EXTRA energy frames,<br>> >> but for the trajectory file (.xtc), there is no extra frames? Am I<br>> >> right?<br>> >><br>> >> "mdrun -h<br>> >> --> The contents will be binary identical (unless you use dynamic load<br>> >> balancing), but for technical reasons there might be some extra energy<br>> >> frames when using checkpointing (necessary for restarts without<br>> >> appending)."<br>> ><br>> > The intent with GROMACS 4.x is for a user to be able to construct a<br>> > .tpr with a very long simulation time, and perhaps constrain mdrun<br>> > with -maxh (or rely on the cluster killing the job), and to use the<br>> > information in the checkpoint file to restart correctly and perhaps to<br>> > then use mdrun -append so that when the simulation is running<br>> > smoothly, only one set of files needs to exist. Thus one doesn't need<br>> > to trouble with using tpbconv correctly, crashes can restart<br>> > transparently, etc. The old-style approach still works, however.<br>> ><br>> > Obviously you should (be able to) verify with mdrun -reprod that<br>> > whatever approach you use when you construct your job scripts leads to<br>> > simulations that are in principle reproducible. For production, don't<br>> > use -reprod because you will want the better speed from dynamic load<br>> > balancing, etc.<br>> ><br>> > Mark<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<br>> > posting!<br>> > Please don't post (un)subscribe requests to the list. Use the www<br>> > 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>> <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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