Re: [ESPResSo] activate PBC explicitly

[Olaf Lenz]

Hi!

Ahmad A. J. Agung wrote:
> ... I found that some particle 
> position actually out of box . What I want to ask are:
> 1. Does Espresso automatically do any analyze (e.g. rdf, rg, energy, 
> pressure, etc) by applying pbc? Or we should add any command to activate 
> pbc.

PBC is the default in Espresso. If you don't use PARTIAL_PERIODIC, the 
system will be fully periodic in all directions. Of course, all 
integration, analysis etc. are supposed to heed this correctly.
As for the positions outside the box, please read the corresponding FAQ 
entry:
http://espressowiki.mpip-mainz.mpg.de/wiki/index.php/FAQ#Some_coordinates_are_outside_of_the_box.21

> Does anyone can help or suggest me, what made the particle position at
> both script will be diiferent after integration?

The positions of two intergration steps are different, as Espresso is 
using a Langevin thermostat by default, which has a random component.

> 3.Does all above have connection with PARTIAL PERIODIC feature?

No. PARTIAL_PERIODIC is important if you do NOT want periodicity in all 
or some directions. Otherwise, the system is always periodic.

Olaf