[gmx-users] g_helix

Kai Zhuang kai.zhuang at gmail.com
Wed May 25 22:52:45 CEST 2005

i have an idea for checking the rotation on a specific segment,
u should be able to implement it on a larger scale by calculating the
mean and deviation or such:

for before simulation:
find a backbone carbon of interest C1.  find it's cordinate.
find an atom immediately attached to it.  find it's cordinate.
calculate the vectors in between.  (yes need math)

for after the simulation, do the same thing.

the two vectors should span a arc, which is ur degree of rotation of phi.

repeat for psy

anyways, the above is a lot of work, you might be able to find a
program that is rewritten to calculate psy and phi factors, which is
the degrees of rotation.  (my biochemistry is crude, so i apologize if
i used the wrong greek letter, but u get the idea)

On 5/25/05, Prasad Gajula <prasad.gajula at uni-osnabrueck.de> wrote:
> Dear Gromacs users,
> How can I check any rotation of backbone if any, after simulation when
> compared to original structure (backbone region at any particular residue
> for example)
> I tried but not able to see quntitatively...
> i can see some changes at particular residue with VMD. but how can prove it.
> looking forward for any help!
> thanking you!
> best regards
> gajula
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Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com

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