[gmx-users] Alpha-Helix Dipole

gtroiano at if.usp.br gtroiano at if.usp.br
Thu Aug 30 10:48:36 CEST 2007

 Thank you for the guidance, David. Now I got it, but a thing that also helped
was to set the option -pbc inbox in trjconv, which I didn't know if I had to (I
read the manual, but even so, I didn't know). Now I see the water dipole
counterbalances the entire protein one (I was testing in PolyALA, so no effect
of the residues. Now I'll test in my helix)

 Thank you again,

> 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)
>   Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> --
> 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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