[gmx-users] Helicity

Diogo Vila Viçosa diogo.vicosa at fc.ul.pt
Fri Feb 6 21:11:41 CET 2015

I Shivangi,

There are several ways to calculate the average helicity. If you are using
linux you can easily do that with a simple awk / bash script. In windows
you can paste the number of residues in helical structure over time in an
excel spreadsheet and calculate the average, etc..

I suppose you are using linux and my advice to you is: "try to learn
something about awk, sed, bash, etc... before you dive in into more complex
things such as a MD simulation".

Best regards,
Diogo Vila Viçosa

shivangi nangia <shivangi.nangia at gmail.com> escreveu no dia Fri Feb 06 2015
at 20:00:41:

> Hello gmx-users,
> I want to calculate the average helicity of a peptide in last 20 ns of the
> simulation.
> g_helix is giving % helicity per residue during the specified period of
> time.
> Is there a way to do what I wish to calculate.
> Kindly help.
> Thanks,
> sxn
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