[gmx-users] Elastic network model

[Mark Abraham]

On 1/09/2012 4:42 AM, mohan maruthi sena wrote:
>   Hi all,
>               I have built topology for elastic network as follows(the
> atoms which fall with in a distance less than 6 angtroms are bonded).
> [bonds]
> ;ai    aj   funct               bo     kb
> 2       1       1       3.80444752888   61.9
> 3       1       1       5.10184956658   61.9
> 3       2       1       3.69916125628   61.9
> 4       1       1       4.19781502689   61.9
> 4       2       1       5.90237528458   61.9
> 4       3       1       3.92569102197   61.9
> 5       1       1       5.30324730708   61.9
> 5       3       1       5.2694262496    61.9
> 5       4       1       3.83092403997   61.9
> 6       3       1       4.07288043036   61.9
> 6       4       1       5.48720921781   61.9
> 6       5       1       3.71358990735   61.9
> 7       3       1       5.51608248669   61.9
> 7       6       1       3.8682865716    61.9
> 8       7       1       3.8047721351    61.9
> 9       8       1       3.81975719124   61.9
> 10      9       1       3.72026195314   61.9
> 11      10      1       3.76893910802   61.9
> 12      11      1       3.8123865229    61.9
> 13      12      1       3.78850801768   61.9
> 14      13      1       3.69171193351   61.9
> 15      13      1       5.42834818338   61.9
> 15      14      1       3.83449357804   61.9
> 16      13      1       5.10757946585   61.9
> 16      15      1       3.83922544272   61.9
> 17      11      1       5.71881902144   61.9
> 17      12      1       4.83263696133   61.9
> 17      13      1       5.48196032456   61.9
>
> The above one is part of topology file. I have 372 residues in my
> protein. when i run equilibration i got the following error
> A list of missing interactions:
>      Bond . of   1027 missing      1
>
> -------------------------------------------------------
> Program mdrun_d, VERSION 4.5.5
> Source code file: domdec_top.c, line: 173
>
> Software inconsistency error:
> Some interactions seem to be assigned multiple times
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors.
>
> None of the interactions are repeated multiple times, when i check the
> log file the following error is written
> Not all bonded interactions have been properly assigned to the domain
> decomposition cells
>
> A list of missing interactions:
>         Bond. of   1027 missing      1
>
> -------------------------------------------------------
> Program mdrun_d, VERSION 4.5.5
> Source code file: domdec_top.c, line: 173
>
> Software inconsistency error:
> Some interactions seem to be assigned multiple times
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Error
>
>
> Can you suggest me what does this error mean . Is the topology correct
> (built) with respect to  elastic network model.

It means your system is 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up. Maybe your 
velocities are far too large for your tiny bond stiffness constants, or 
your integration step was too large, or probably a dozen other things we 
can only guess at because we don't know your initial configuration or 
your .mdp file contents. If you're just inventing stuff on your own, 
then I suggest you find an actual elastic network model of which someone 
else has already published a dynamical model, and work out how to 
implement that, instead of hoping someone will tell you how an actual 
elastic network model works. Only then do you have some basis for 
seeking to do something novel.

Mark