Re: [ESPResSo-users] radius of gyration

[Stefan Kesselheim]

Hi Roya,
why are you worried?
Last time I wrote:
rg is a fluctuating quantity, that depends on the conformation of the polymer 
(you could say, rg describes how extended a certain polymer conformation is). 
You probably want to obtain the mean value, which people tend to call the 
"radius of gyration of a polymer".

If you look at your polymer in vmd, you'll see that it fluctuates. The radius 
of gyration is not constant, but can change a lot. Look up the definition, and 
you will see that it is a function of all monomer positions. As they can 
fluctuate, the radius of gyration fluctuates.

Please don't forget: This is the Espresso users mailing list. People here 
gladly help with Espresso-related questions, but we can not be your scientific 
advisors.

Cheers
Stefan

On May 8, 2014, at 12:24 PM, roya moghaddasi <address@hidden> wrote:

> 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"
> 
> The problem is that the rg fluctuates a lot, for example it goes from 16 to 8 
> gradually, but finally it gets back to 16, again.
> I would appreciate if anyone could help me solve this problem.
> Cheers,
> Roya