Re: [ESPResSo-users] constraint pore

[Florian Weik]

Hi,

this is a known bug in the pore contraint. As you found out setting an outer radius typically fixes this. If you want the pore do block the hole box, just set an outer radius slightly larger than the box size. This will be fixed in the next release of

Espresso. Unfortunately this is not fixed in the current developer version so trying

that won't help you.

Cheers,

Florian

On Wed, Aug 17, 2016 at 11:55 AM 93200347 <address@hidden> wrote:

To whome it may concern

Hi,

sorry for asking again,it would be so nice if you could help me on this topic.I had this question emailed a few days ago,unfortunatly the problem stil exists and I was unable to find anyone else helping me solving this  issue.

I,ve been using older versions up to espresso 3.2.0 and my code was okay in them but I encountered a problem using latest version 3.3.1.

I.ve been using constraint pore for translocation with following syntax:

 constraint pore center $x_pore $y_pore $z_pore axis $x_axis $y_axis $z_axis radius $rad length [expr $leng/2]  type 2
  constraint wall dist 0. normal 1.0 0. 0. type 2

But in new version I used this instead:

 constraint pore center $x_pore $y_pore $z_pore axis $x_axis $y_axis $z_axis radius $rad length [expr $leng/2]  type 2

According to the ug, these syntaxs should be similar.

when I translocate particle from the right side to the left side after the middle recieve this error:

particle cordinate out of range& constraint pore violated by particle.

when I translocate particle from the left side to the right side near the pore recive this error:

particle coordinate out of range.

when I consider outer _rad solve this errors!!!!

Since I didn,t recive any error modeling the same system in previous version,can this problem been caused by software bugs in 3.3.1?

would you please explain the geometry of pore in 3.3.1?

Thanks for your time and consideration,your help our  so vital for me.I will appreciate any guidance from you.

sincerely yours,

zeinab