[gmx-users] Generate topology for infinite alpha helix with pbc?

Zhiping Xu xuzp at MIT.EDU
Mon Apr 13 20:37:24 CEST 2009

Hi all:
I have a basic question here. I want to simulate a infinite alpha-helix protein, say alanine represented using a unit cell containning 11 residues.
Now I want to simulate it in GROMACS but don't know how to generate TOP for the structure, i.e. the connectivity between the 1st residue and image of 11th residue. Conventional TOP generation process using pdb2gmx will terminated them rather than fit my need.
Could anyone here give me a hand? Thanks.
XU Zhiping, Ph. D
Civil and Environmental Engineering
MIT, Cambridge, MA 02139
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