[gmx-users] Helicity

[shivangi nangia]

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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>