Hi ALL,<div><br></div><div>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:</div>
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<div><div> Energies (kJ/mol)</div><div> Bond G96Angle Proper Dih. Improper Dih. LJ (SR)</div><div> 4.73694e+04 3.00928e+04 4.68451e+03 8.26028e+02 -1.29727e+06</div><div> Coulomb (SR) Potential Kinetic En. Total Energy Temperature</div>
<div> -7.97216e+03 -1.22227e+06 2.24656e+05 -9.97613e+05 3.21675e+02</div><div> Pressure (bar) Cons. rmsd ()</div><div> -9.97540e+00 1.69233e-05</div><div><br></div><div><br></div><div>Not all bonded interactions have been properly assigned to the domain decomposition cells</div>
<div><br></div><div>A list of missing interactions:</div><div> G96Angle of 28064 missing 1</div><div><br></div><div>Molecule type 'DSPC'</div><div>the first 10 missing interactions, except for exclusions:</div>
<div> G96Angle atoms 10 11 12 global 5309 5310 5311</div><div><br></div><div>-------------------------------------------------------</div><div>Program mdrun_mpi, VERSION 4.0.7</div><div>Source code file: domdec_top.c, line: 341</div>
<div><br></div><div>Fatal error:</div><div>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</div>
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</div><div><br></div><div>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:</div><div><br></div><div>--------------------------------------------------------------------------------------------------------------</div>
<div><div>[ system ]</div><div>PROT in DSPC Bilayer</div><div><br></div><div>[ molecules ]</div><div>Protein 1</div><div>DSPC 104</div><div>W 1397</div><div>NA+ 0</div><div>CL- 4</div>
<div>Protein 1</div><div>DSPC 104</div><div>W 1397</div></div><div>NA+ 0</div><div>CL- 4</div><div>-------------------------------------------------------------------------------------------------------------</div>
<div><br></div><div>How can I resolve this error? Any suggestion is welcome.</div><div><br></div><div>Regards,</div><div><br></div><div>Anirban</div>