[gmx-users] Generalized order parameter S2

Dilraj Lama dennis at iitk.ac.in
Fri Aug 17 17:06:47 CEST 2007

Hello gmx-users,
               I have a query regarding the generalized order paprameter
S2.I have performed a 50ns simulation of a protein in
solution.I now want to calculate the order parameter S2 of
the protein from the trajectory.I looked through the
mailing list to get an idea on how to go about calculating
the property.

I collected information that the tools "g_chi" and "g_rotacf" can help me
perform the task.

g_chi uses Phi, Psi and Omega angles to calculate it.

g_rotacf can calculate it with respect to N-H bond angle.

Which of the two approach would be more appropriate?

Also using "g_rotacf" I am still not very clear on how to go about using
the  tool.

Can anyone who has previuosly performed this calculation help me out.

I look forward to your responses.

Thank you.

Dilraj Lama,
Graduate student,
Bioinformatics and Biomolecular Simualtion lab,
Dept. of BSBE;IITK-kanpur,
Uttar pradesh,India-208016.
email:dennis at iitk.ac.in,dilraj2002 at yahoo.com

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