[gmx-users] separation of two strands of DNA during of simulation

[Mark Abraham]

----- Original Message -----
From: shahab shariati <shahab.shariati at gmail.com>
Date: Sunday, May 30, 2010 16:28
Subject: [gmx-users] separation of two strands of DNA during of simulation
To: gmx-users at gromacs.org

> Dear Justin
>  
> thanks for your attention.
>  
> You said that separation of two strands of DNA during of simulation is a normal consequence of periodic boundary conditions. I had used periodic boundary condition in mdp file as following:

No, he didn't say separation was a consequence of PBC. *Apparent* separation can be. I'm sure he provided this link, but make sure you read it, please :-) http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark
  
> Periodic boundary conditions:
> pbc              = xyz
>  
> Should I delete pbc from mdp file?
>  
> Whether elimination of pbc prevents separation of two strand of DNA?