[gmx-users] Polymer in periodic boundary conditions

Ester Chiessi ester.chiessi at uniroma2.it
Wed Oct 23 16:51:47 CEST 2002

Hi gromacs users,

I'm trying to build an infinite chain in periodic boundary conditions..

I saw I have to use:


The question is how to insert in the topology file the information that
the last atom of the chain has to be covalently bound to the periodic
image of the first .

Should I have to use the same residue name for each repetitive unit (
i.e. no end-residues) only giving the connectivity to the preceeding
residue and then choose the exact box lenght to contain the part of the
chain I'm defining in the topology?

Is it important to start with an orientation of the chain which
geometrically satisfies the periodicity requirement?

Is it possible to solvate the polymer and use the PBC jet?

Thanks for your help.


Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462

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