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Re: [ESPResSo-users] radius of gyration
From: |
Stefan Kesselheim |
Subject: |
Re: [ESPResSo-users] radius of gyration |
Date: |
Thu, 8 May 2014 12:31:36 +0200 |
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