calculation of helical axis in NAMD

From: Dhiraj Srivastava (
Date: Sat Apr 07 2018 - 01:01:20 CDT

   I want to calculate helical axis of an alpha-helix of my protein along
which I want to rotate that particular helix with respect to rest of the
protein. is there any build in function in namd that I can use to calculate
it or do I need to write the script to do it? also during the simulation,
the atoms in alpha helix will move, changing the helical axis. so do I need
to keeps calculating and updating the axis of rotation or will it be safe
to calculate it at the beginning of the simulation and don't change it
during the simulation? if I am calculating the helical axis on the the fly
during simulation, will it slow down the simulation significantly?

Thank you

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