[gmx-users] infinite alpha-helix

David spoel at xray.bmc.uu.se
Wed Dec 1 17:19:38 CET 2004

On Wed, 2004-12-01 at 16:03 +0100, herbst at fhi-berlin.mpg.de wrote:
> Hello all!
> Is it possible to create the illusion of an infinite alpha-helix by
> choosing the box size so, that the outer atoms of the helix (which are
> restrained, of course) touch the box sides and PBC makes it appear
> infinite? Can the box be choosen in that way or has there to be a distance
> between atoms and the box side?
Yes you can do it, but it is tricky how to get the topology. If you have
a topology you can simulate it with

> Thanks for your answers,
> Anna
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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