[gmx-users] Polymers in PBC

[Ester Chiessi]

David van der Spoel wrote:

> On Mon, 2003-03-31 at 13:05, Ester Chiessi wrote:
> > Dear Gromacs users,
> >
> > I'm working to calculate MD trajectories for a polymer network in water. I built the topology so that chemical bonds across boundaries are mantained.
> >
> > At the present I could minimize the system and calculate about 40 ps of dynamics, with timestep 0.5 fs, T 303 K with Berendsed and no pressure coupling and constraining by Shake only X-H bonds.
> > In the md log file the following message is printed every ten steps:
> >
> > There were 6 inconsistent shifts. Check your topology
> >
> > (This warning is related to the 'infinite' connectivity, because it is absent if I remove it from the topology)
> >
> > Total energy showed I was near to the equilibration when the program suddenly stopped for segmentation fault, without saving coordinates and giving other explanations.
> >
> > I'd like to know if anyone succesfully performed MD in on similar systems, before giving up my hope!
> >
> try running again with an environment variable set:
> setenv GMXFULLPBC 1

I forgot to say I always worked so.

>
>
> > Thanks,  Ester.
> >
> > --
> > 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,        Dept. of Cell & Mol. Biology
> Husargatan 3, Box 596,          75124 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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--
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