[gmx-users] Alpha-Helix Dipole

[David van der Spoel]

gtroiano at if.usp.br 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
> 
> 
>> 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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> 
> 
> 
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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