[gmx-users] about periodicity removal....

Justin A. Lemkul jalemkul at vt.edu
Sat Feb 25 16:23:30 CET 2012

rama david wrote:
> Hi GROMACS friend,
>                   Thank you Justin For guidance.
>  As I also doing your KALP-15 in DPPC tutorial,
> In that you maintain remove initial periodicity of
> DPPC.. 
>           What is means initial periodicity??

The molecules of DPPC were post-processed in such a way that their atoms were 
split across periodic boundaries.

> That is the reason I thought the peptides have
> Initial periodicity.(As periodic box is seen in pymol)..!!!

The fact that you can see (or render) a periodic box is not a problem, quite the 
contrary.  Using periodic boundary conditions is commonplace, but only in 
certain situations is it necessary to undo their effects.  It does not sound to 
me like this is the case in your situation.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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