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
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