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.nan...@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.vic...@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.nan...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.
