Re: [ESPResSo] Re: Radius of Gyration

[Axel Arnold]

On Sunday 09 December 2007, Lorenzo Isella wrote:
> Hello,
> Yes, unfortunately at this point I am rather sure. For a small system,
> 10 particles, you can follow even by eye on VMD what is happening to
> your particles and I also tried extending quite a lot the integration
> time, but the result did not change.
> Obviously something is going wrong...any suggestion here is really
> appreciated.
> Cheers

Hi Lorenzo!

as Markus already pointed out, the problem are the periodic boundary 
conditions. For polymers, the radius of gyration should be calculated with 
_unfolded_ coordinates, and that is what ESPResSo does. Otherwise, a polymer 
crossing a boundary will have a huge radius of gyration.

However, the VMD output is by default folded. Therefore, you can see in VMD a 
nice cluster, even if for the calculation of the radius of gyration, it is 
wildly scattered in different cells. To check this, use imd 
positions -unfolded or write a pdb-file, which has unfolded coordinates by 
default.

Apart from that, calculating a meaningful radius of gyration is non-trivial in 
your case. You cannot simply use the folded coordinates to calculate the rg, 
because your cluster could also be located across a boundary. With folded 
coordinates, that would look like two smaller clusters at the box boundaries.

Many regards,
Axel


-- 
Dr. Axel Arnold
FOM Institute for Atomic and Molecular Physics
Kruislaan 407                           Phone: +31 20 6081 275
1098 SJ Amsterdam, The Netherlands      E-mail: address@hidden