[gmx-users] separation of two strands of DNA during of simulation
mark.abraham at anu.edu.au
Sun May 30 09:40:13 CEST 2010
----- 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
> Periodic boundary conditions:
> pbc = xyz
> Should I delete pbc from mdp file?
> Whether elimination of pbc prevents separation of two strand of DNA?
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