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

[Anirban Ghosh]

Thanks a lot XAvier for clarifying my doubt. You mean to say "-rdd" option
with mdrun, right? And why does this curvature of the membrane occurs?

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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