[EMAIL PROTECTED] 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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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