[gmx-users] MD of polymer in pbc

[K.A. Feenstra]

Ester Chiessi wrote:
> Thanks for your support.
> 
> I'll study the geometrical detail of my molecules before the dynamics.
> 
> Only a thing:
> I found in the Gromacs 3.1.1 manual (pg. 29) that all the eigenvalues of the matrix An,
> used by the algorithm LINKS, must be smaller than 1. This is not verified in molecules
> with 'high' connectivity.
> Could my problems be explained with the uncompatibility with LINKS (my molecule is 'a
> ring structure' )?

Probably not. The 'high connectivity' that the manual mentions is
the connectivity between adjacent constraints, e.g. in a butane with
all bond lengths and also all angles constrained. Here the middle
bond constraint is connected to four other constriants (the two outer
bonds, and the two angles). In the approximated matrix inversion that
Lincs performs, this connectivity leads to over-correction. However,
in your 'loosely' connected molecule, this should not be a problem.


-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
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