Hi. I guess g_polystat can't do that. The online reference for gmx polystat (( http://manual.gromacs.org/programs/gmx-polystat.html) says: "...the persistence length is defined as number of bonds where the average cos reaches a value of 1/e."
The number of bonds is one number. I don't think it is possible to recover the many cos(theta) used to calculate this number of bonds. How about g_angle? (http://www.cenapad.unicamp.br/parque/manuais/Gromacs/online/g_angle.html) (http://manual.gromacs.org/programs/gmx-angle.html) On Sat, Sep 12, 2015 at 2:33 AM, soumadwip ghosh <soumadwipgh...@gmail.com> wrote: > Dear all, > I want to calculate the persistence length of a single stranded > DNA in the presence of various salts. I want to plot a lnP(theta) vs > 1-cos(theta) graph, where theta is the bend angle of the DNA and P(theta) > is the angular probability. From GROMACS what I obtained was as follows- > > # This file was created Thu Sep 3 07:02:19 2015 > # by the following command: > # g_polystat -f mdfinal_60ns.xtc -s mdfinal_60ns.tpr -p persist_18mm.xvg > # > # g_polystat is part of G R O M A C S: > # > # GRoups of Organic Molecules in ACtion for Science > # > @ title "Persistence length" > @ xaxis label "Time (ps)" > @ yaxis label "bonds" > @TYPE xy > 0.000 0.4025 > 2.000 0.4472 > 4.000 0.4527 > 6.000 0.4958 > 8.000 0.4444 > 10.000 0.5157 > 12.000 0.5164 > 14.000 0.5471 > 16.000 0.5090 > > Here, the time evolution of some bonds are given. Can anyone help resolving > the issue? > > Thanks in advance, > Soumadwip Ghosh > Research Fellow, > IITB > Mumbai > India > -- > 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.