[gmx-users] MD of polymer in pbc

[Ester Chiessi]

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' )?

Thanks

Ester



K.A. Feenstra wrote:

> Ester Chiessi wrote:
>  > Hi Gromacs people,
>  >
>  > I'm working to perform molecular dynamics simulations of a polymer in PBC and I
>  > found some problems.
>  >
>  > After preliminary minimizations and preparations of the system (with no problem if
>  > I don't insert the connectivity accross boundaries), I received this message during
>  > the minimization of the 'infinite' chain:
>  > ...........
>  > Removing pbc first time.
>  > There were 2 inconsistent shifts. Check your topology.
>
> [...]
>  > Step -2, time -0.004 (ps)  LINCS WARNING
>  >  atom 1 atom 2  angle  previous, current, constraint length
>  >       1      2   88.9    0.1527   0.4141      0.1530
>  >      38      1   97.4    0.1510   1.0500      0.1530
> [...]
>  > Step -1, time -0.002 (ps)  LINCS WARNING
>  >  atom 1 atom 2  angle  previous, current, constraint length
>  >       1      2  105.5    0.4141   0.2115      0.1530
>  >      38      1   96.1    1.0500   0.0735      0.1530
> [...]
>
> You have bonds that should be 0.15 nm in length, but they vary
> from 0.07 (half what it should be) to 1.05 (seven times too large).
> That is serious. My first assumption would still be what I
> suggested before: your polymer conformation is not minimized
> well enough. It should first be minimized as a *finite* molecule,
> to remove all internal strain, and subsequently as an *infinite*
> molecule, in combination with adjusting the box dimension. But,
> by now you probably did that already. My only remaining advice
> is to check all the steps that you did up to now (i.e. look at all
> the intermediate structures, check the bonds and angles by hand,
> using e.g. rasmol, etc.), and hope that someone else on the list
> with experience in infinite molecules can help you further... ;-)
>
> --
> Groetjes,
>
> Anton
>   ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> | (    ) |-----------------------------------------------------------|
> |  \__/  | "If You See Me Getting High, Knock Me Down"               |
> |        | (Red Hot Chili Peppers)                                   |
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--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
       39*6*72594874
Fax:39*6*72594328