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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Jan 9 19:44:08 CET 2010

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?

Thank you,

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 */

...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.


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