[gmx-users] Helicity

[Diogo Vila Viçosa]

I am not sure if I can give you the most adequate answer because I am not
in a computer with GROMACS right now.

I think that the easiest way to do that is by using the do_dssp command
which gives you the number of residues in helix, b-sheet, etc, over time
and then do the average of the corresponding column.

Regards,
Diogo




shivangi nangia <shivangi.nangia at gmail.com> escreveu no dia Fri Feb 06 2015
at 20:42:52:

> 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
>
> ..........................so on
>
> 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.
>
> Thanks,
> sxn
>
>
>
> On Fri, Feb 6, 2015 at 3:11 PM, Diogo Vila Viçosa <diogo.vicosa at fc.ul.pt>
> wrote:
>
> > 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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