[gmx-users] Polymers in PBC

[David van der Spoel]

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

> 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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