<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
--></style>
</head>
<body class='hmmessage'>
Hi,<br><br>Indeed I forgot to add a pbc call for confout in EM.<br>I fixed it for the next release.<br><br>Note that the broken molecules are not a problem for Gromacs programs,<br>but for visualization you might want to use trjconv -pbc mol.<br><br>Berk<br><br>> Date: Sat, 9 Jan 2010 17:58:43 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] confout.gro contains PBC-broken molecules after EM in parallel with domain decomposition<br>> <br>> <br>> <br>> On 1/9/10 1:44 PM, chris.neale@utoronto.ca wrote:<br>> > Hi Justin,<br>> ><br>> > I can confirm that I see that code snippet in my md.c code, although my<br>> > tests indicate that this is not the end of the story.<br>> ><br>> > I have now taken the output .gro, ran it through trjconv -pbc mol and<br>> > then ran mdrun again under a variety of conditions:<br>> ><br>> > 1. EM(steep) mdrun_mpi NP=8 -dd (BROKEN) *ran twice*<br>> > 2. EM(steep) mdrun_mpi NP=8 -pd (whole)<br>> > 3. EM(steep) mdrun NP=1 (whole)<br>> > 4. MD mdrun_mpi NP=8 -dd (whole)<br>> > 5. MD mdrun_mpi NP=8 -pd (whole)<br>> > 6. MD mdrun NP=1 (whole)<br>> > 7. EM(cg) mdrun_mpi NP=8 -dd (BROKEN)<br>> > 8. EM(l-bfgs) mdrun_mpi NP=8 -dd (n/a)<br>> > error: Cannot do parallel L-BFGS Minimization - yet.<br>> ><br>> > The tests above were with nsteps=500, so I ran one more steep EM with<br>> > mdrun_mpi NP=8 -dd and found that confout.gro was indeed broken over PBC<br>> > even with only a single step (nsteps=1).<br>> ><br>> > Justin: Can you confirm that you can run a steep EM under mdrun_mpi NP=8<br>> > with domain decomposition and obtain a confout.gro that is not broken<br>> > over PBC?<br>> ><br>> <br>> Indeed, you're quite right. The few systems I had at hand when I posted earlier <br>> were all proteins in water, so nothing was crossing PBC. My lipid systems <br>> indeed are still broken after EM.<br>> <br>> It looks like the confout writing was fixed in mdrun.c, but perhaps not for the <br>> minimization routines? Would this be in minimize.c? I tried looking through <br>> the source a bit, but couldn't come up with a fix. Too much of a novice :) <br>> Maybe this one is worth a bugzilla? Probably one of the developers could fix <br>> this in about half a heartbeat.<br>> <br>> -Justin<br>> <br>> > Thank you,<br>> > Chris.<br>> ><br>> > On 1/9/10 11:25 AM, chris.neale at utoronto.ca wrote:<br>> >> Hi Justin,<br>> >><br>> >> I just double checked and certainly the confout.gro from my EM run in<br>> >> parallel with domain decomposition in mdrun is broken over periodic<br>> >> boundaries.<br>> >><br>> >> I'm running gromacs-4.0.5 on a nehalem under openmpi. Here is my .mdp<br>> >> file<br>> >><br>> ><br>> > That's really weird. None of my 4.0.x runs have had that problem. Now, I<br>> > am no<br>> > C expert, but I found the following in md.c (taken from the 4.0.5 source):<br>> ><br>> > fprintf(stderr,"\nWriting final coordinates.\n");<br>> > if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr)) {<br>> > /* Make molecules whole only for confout writing */<br>> > do_pbc_mtop(fplog,ir->ePBC,state->box,top_global,state_global->x);<br>> ><br>> > ...after which confout.gro is written.<br>> ><br>> > There are no such lines in the 4.0 source, so I think this was added<br>> > over the<br>> > course of later development.<br>> ><br>> > I don't know what's going on with your system(s); maybe we should<br>> > continue any<br>> > other discussion in a new thread, so we don't hijack this one :) There<br>> > are also<br>> > several entries in the list archive where users have spotted broken<br>> > frames in<br>> > the trajectory, but an intact confout.gro.<br>> ><br>> > -Justin<br>> ><br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<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 />New Windows 7: Simplify what you do everyday. <a href='http://windows.microsoft.com/shop' target='_new'>Find the right PC for you.</a></body>
</html>