[gmx-users] Making sure I understand an error

[XAvier Periole]

You are right. With MARTINI you often need an rdd bigger than default.  
1.4 is reasonable.

On Jun 29, 2009, at 19:33, Michael Lerner <mglerner+gromacs at gmail.com>  
wrote:

> Hi,
>
> I have a 72-lipid DPPC (MARTINI) system that I ran for 400ns in  
> GROMACS 3.3.3. I picked a snapshot from the middle (~100ns), so I  
> know it should be equilibrated and be able to run for several  
> hundred nanoseconds. If I use GROMACS 4.0.3 (or 4.0.5) and 1, 2, or  
> 4 processors, everything is great. However, if I use more than 4  
> processors (either on a single node or on two nodes), I get errors  
> like this:
>
> ------------- begin error -------------
> vol 0.87  imb F  2% step 350900, will finish Sat Jun 27 23:16:51 2009
> vol 0.84  imb F  4% step 351000, will finish Sat Jun 27 23:16:49 2009
>
> A list of missing interactions:
>             G96Angle of    576 missing      1
>
> Molecule type 'DPP'
> the first 10 missing interactions, except for exclusions:
>             G96Angle atoms    2    3    5      global   254   255    
> 257
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.5
> Source code file: domdec_top.c, line: 341
>
> Fatal error:
> 1 of the 1368 bonded interactions could not be calculated because  
> some atoms involved moved further apart than the multi-body cut-off  
> distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see  
> option -rdd, for pairs and tabulated bonds also see option -ddcheck
> -------------------------------------------------------
>
> "Pump Up the Volume Along With the Tempo" (Jazzy Jeff)
>
> Error on node 0, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 0 out of 8
>
> gcq#177: "Pump Up the Volume Along With the Tempo" (Jazzy Jeff)
>
> h199:0.MPID_Abort: h199:0.MPI Abort by user Aborting program !
> h199:0.MPID_CH_Abort: h199:0.Aborting program!
> Abort on node h199 due to MPI_Abort (type 2)
> -------------- end error --------------
>
> This error happens on a different step depending on how many  
> processors I use, whether I use gfortran or ifort, etc.
>
> Am I understanding correctly that I have a triplet of particles A-B- 
> C where the bond-angle term cannot be calculated because the  
> distance between A and C is greater than 1.2 nm?
>
> Is dynamic load balancing causing the error to happen at different  
> steps for different numbers of processors?
>
> It appears that I can fix the problem by setting -rdd=1.4 on the  
> command line, but I'd like to make sure I'm not just sweeping  
> something else under the rug.
>
> For what it's worth, the equilibrium bond lengths in MARTINI's DPPC  
> model are all either .47 or .37 nm. In the -rdd=1.4 run, the maximum  
> bond lengths range from .68 to .71 nm depending on the particular  
> bond and the A-C distances from the A-B-C triplets range from 1.09  
> to 1.21.
>
> Also, is there any chance that the default settings will get this  
> right for my system in the future?
>
> Thanks,
>
> -michael
>
> -- 
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
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