[gmx-users] Polymers in PBC

[Ester Chiessi]

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!

Thanks,  Ester.

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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