[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

[Justin A. Lemkul]

Anirban Ghosh wrote:
> Hi ALL,
> 
> I have made a CGMD system with multiple copies of a single protein in 
> bilayer, by replicating the monomer using genconf in the X-Y plane. 
> After running CGMD for about 100 ns, I am getting the following error:
> 
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>    Energies (kJ/mol)
>            Bond       G96Angle    Proper Dih.  Improper Dih.        LJ (SR)
>     4.73694e+04    3.00928e+04    4.68451e+03    8.26028e+02   -1.29727e+06
>    Coulomb (SR)      Potential    Kinetic En.   Total Energy    Temperature
>    -7.97216e+03   -1.22227e+06    2.24656e+05   -9.97613e+05    3.21675e+02
>  Pressure (bar)  Cons. rmsd ()
>    -9.97540e+00    1.69233e-05
> 
> 
> Not all bonded interactions have been properly assigned to the domain 
> decomposition cells
> 
> A list of missing interactions:
>             G96Angle of  28064 missing      1
> 
> Molecule type 'DSPC'
> the first 10 missing interactions, except for exclusions:
>             G96Angle atoms   10   11   12      global  5309  5310  5311
> 
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.7
> Source code file: domdec_top.c, line: 341
> 
> Fatal error:
> 1 of the 62352 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
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> 
> On visual inspection I found that the bilayer is becoming curved (image 
> attached). In the .top file I have mentioned the different monomers of 
> my system as:
> 
> --------------------------------------------------------------------------------------------------------------
> [ system ]
> PROT in DSPC Bilayer
> 
> [ molecules ]
> Protein     1
> DSPC        104
> W           1397
> NA+         0
> CL-         4
> Protein     1
> DSPC        104
> W           1397
> NA+        0
> CL-         4
> -------------------------------------------------------------------------------------------------------------
> 
> How can I resolve this error? Any suggestion is welcome.
> 

Search the list archive.  This error has come up before, and I know there's been 
at least one instance of it for a CG system.  I believe the answer was to 
increase -rdd (since bonded interactions occur at longer distance in CG 
systems), but please do the search for yourself.

-Justin

> Regards,
> 
> Anirban
> 
> ------------------------------------------------------------------------
> 

-- 
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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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