[gmx-users] Re: Error in Membrane simulations with POPC bilayer

[Justin A. Lemkul]

On 7/13/12 1:44 AM, J Peterson wrote:
> Thanks for the comment. By the way how to make a bigger box at this time of
> the tutorial without affecting any part of the system. Can I use editconf
> with slightly bigger number for z-axis (something like 6.7 which was 5.7
> before)?
>

The box should be sufficiently large so as to avoid spurious interactions across 
periodic boundaries.  The size is thus motivated by the length of the cutoffs 
used.  Increasing the box by 1.0 nm might be just enough, but you should 
calculate this very carefully.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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