[gmx-users] help with periodic boundary conditions

[Justin A. Lemkul]

Jarol E. Molina wrote:
> Hi all
> 
> I am simulating a polymer chain and I need some help. At some simulation 
> time, the polymer chain is outside the simulation box.
> 
> I know that the option “pbc = xyz” into file grom.mdp is sufficient to 
> have periodic boundary conditions.
> 
> 
> Can you help me
> 
> 

There is no "outside" of a periodic system.  Please consult the wiki on the subject:

http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions

-Justin

> Thanks
> 
> 
> 
> -- 
>               Jarol E Molina, I.Q., M.S.
> Estudiante Doctorado en Ingeniería - Sistemas Energéticos
> Universidad Nacional de Colombia - Sede Medellín
> jemolina at unal.edu.co <mailto:jemolina at unal.edu.co>
> jemolina at unalmed.edu.co <mailto:jemolina at unalmed.edu.co>
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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