[gmx-users] MD of polymer in pbc

[David van der Spoel]

On Tue, 2002-11-26 at 14:18, 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' )?


maybe, you can always modify the algorithm for constraints to shake
> 
> 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
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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