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

[XAvier Periole]

On Aug 16, 2010, at 1:33 PM, Anirban Ghosh wrote:

> Thanks a lot XAvier for clarifying my doubt. You mean to say "-rdd"  
> option with mdrun, right?
yes
> And why does this curvature of the membrane occurs?
No idea!
>
> Thanks a lot once again.
>
> Regards,
>
> Anirban
>
> On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole <x.periole at rug.nl>  
> wrote:
>
> Although a bit worrying the curvature of your bilayer is not
> responsible for the error message you are seeing.
>
> to solve the problem you have to increase to use the -rrd option
> (see manual for explanation). Typicaly a value of 1.4 to 1.6 should
> be fine.
>
>
> On Aug 16, 2010, at 12:16 PM, 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.
>
> Regards,
>
> Anirban
> <sim.jpeg>--
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