[gmx-users] confout.gro contains PBC-broken molecules after EM in parallel with domain decomposition

[Berk Hess]

Hi,

Indeed I forgot to add a pbc call for confout in EM.
I fixed it for the next release.

Note that the broken molecules are not a problem for Gromacs programs,
but for visualization you might want to use trjconv -pbc mol.

Berk

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