Re: [gmx-users] calculation of persistence length

2015-09-13 Thread Johnny Lu
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

[gmx-users] calculation of persistence length

2015-09-12 Thread soumadwip ghosh
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