[gmx-users] Alpha-Helix Dipole

David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 29 20:11:43 CEST 2007

gtroiano at if.usp.br wrote:
>  Hi David
>  Thank you very much for the reply! So, which group, in the end, shall I select
> in g_dipoles to see the dipole? And how to use trjconv after editconf the way
> you told me? (the input/output of editconf is a .gro file and of trjconv is
> .trr/.xtc files) And whose group shall I select in the least squares/output
> prompts in trjconv -fit trans+rot?
>  Thank you very much,
>  Gustavo
I would do both the helix backbone, and the entire helix, so that you 
can test whether the sidechains compensate for the net dipole or the 
other way around. You could also look at the net dipole of the water 
with resect to the helix.

As for trjconv, please read the manual about aligning structures 
(trjconv -h)

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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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