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[ESPResSo-users] setmd time and rg

From: roya moghaddasi
Subject: [ESPResSo-users] setmd time and rg
Date: Tue, 6 May 2014 23:45:23 -0700 (PDT)

Hello everybody,
I have 40 100-length polymer in my system and I want to calculate the radius of gyration of them, so I wrote these lines in my program:
    analyze set chains 0 40 100
    set rg1  [lindex [analyze rg 0 1 100] 0], this is to calculate the rg of just one polymer, is it right?
    set rg2 [lindex [analyze rg] 0], this is to calculate the rg of all the polymer, is it right?

    puts $obs1 "[setmd time] $rg1"
    puts $obs2 "[setmd time] $rg2"

  I ran my program twice, the first time "setmd time" gives me 499.5 to 5449.5 through 10^6 step, the second time it gives me 2449.5 to 7399.5, why this happens? I thought it should start with the same number and it ends with the another same number each time I run the program since there is no change in my program.

Another question is there are fluctuations in the rg  value, in other words it fluctuates between 10 and 11 a lot and in second run it reaches to 14-15 value from 10-11 value, I am so confused, what does these results mean? why does the value of rg changes in each run, is there any mistake that I made?

I appreciate if someone can help me?

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