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

[Anirban Ghosh]

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
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