shivangi.nangia at gmail.com
Fri Feb 6 21:42:13 CET 2015
Thanks. I am aware of all those commands.
My question is specific to gromacs out, the file helicity.xvg has an output
of the form:
9 @ title "Helicity per Residue"
10 @ xaxis label "Residue"
11 @ yaxis label "% of time"
12 @TYPE xy
13 1 0
14 2 92.6148
15 3 86.8263
16 4 96.008
It is telling me residue 2 is 92 % of time (that I specified) helical.
I want the average helicity of the peptide during the specified time.
On Fri, Feb 6, 2015 at 3:11 PM, Diogo Vila Viçosa <diogo.vicosa at fc.ul.pt>
> 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
> at 20:00:41:
> > Hello gmx-users,
> > I want to calculate the average helicity of a peptide in last 20 ns of
> > 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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