[EMAIL PROTECTED] wrote:
Just one more thing, David. I read the manual, but I couldn't realize: is the
average dipole, (at the top of the g_dipoles output) the overall dipole of the
system? (also in the adip.xvg, plotted against time). Because all I want to
know is whether the system has a low dipole moment (which in the case of
polyala+h2o, the average is 2.3 D)
depends on your index file. the total dipole is also stored in the
energy file, so you can run g_energy to get it out, or g_dipoles -enx to
compute dielectric constants etc.
Gustavo
[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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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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