[gmx-developers] Failing particle decomposition in gmx4.0.4

[Per Larsson]

Hi!

I believe that with particle decomposition, you cannot have  
constraints between the nodes (only implemented with domain decomp).

One trick around this (if you still want pd) would be to increase the  
mass of the hydrogens somewhat, and use constraints=h-bonds, which  
gives you local constraints only. One could of course argue whether  
this is 100% accurate :-)

Cheers
/Per



6 maj 2009 kl. 20.46 skrev Erik Marklund:

> Erik Marklund skrev:
>> Hi,
>>
>> I need to run a series of simulations using gromacs 4 with particle  
>> decomposition. I constrain all bonds with LINCS and submit my job  
>> to the cluster. Both the log-file and my mdp-file show that LINCS  
>> constraints are indeed what is to be used, but mdrun nevertheless  
>> quits with a fatal error and the following message:
>>
>> -------------------------------------------------------
>> Program mdrun_mpi_d, VERSION 4.0.4
>> Source code file: splitter.c, line: 130
>>
>> Fatal error:
>> Shake block crossing node boundaries
>> constraint between atoms (1467,1474)
>> -------------------------------------------------------
>>
>> Shake block? Why on earth does Shake have to do with anything?!  
>> More importantly, how can I fix this?
>>
>> Here's an exerpt from the log-file:
>>  ...
>>  nbfgscorr            = 10
>>  ConstAlg             = Lincs
>>  shake_tol            = 0.0001
>>  lincs_order          = 2
>>  lincs_warnangle      = 30
>>  lincs_iter           = 8
>>  bd_fric              = 0
>>  ...
>>
>> I use gromacs 4.0.4 i double precision compiled from source that  
>> was downloaded from gromacs.org, in other words no funky developer- 
>> version.
>>
> And here's more from the log-file:
> ...
> Initializing LINear Constraint Solver
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
> LINCS: A Linear Constraint Solver for molecular simulations
> J. Comp. Chem. 18 (1997) pp. 1463-1472
> -------- -------- --- Thank You --- -------- --------
>
> The number of constraints is 1984
> There are: 1960 Atoms
> splitting topology...
> There are 698 charge group borders and 1 shake borders
> There are 698 total borders
> Division over nodes in atoms:
>    492     489     488     491
> Walking down the molecule graph to make constraint-blocks
>
> -------------------------------------------------------
> Program mdrun_mpi_d, VERSION 4.0.4
> Source code file: splitter.c, line: 130
>
> Fatal error:
> Shake block crossing node boundaries
> constraint between atoms (1467,1474)
> -------------------------------------------------------
> ...
>
> -- 
> -----------------------------------------------
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>
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