[gmx-users] Re: Error in Membrane simulations with POPC bilayer
Justin A. Lemkul
jalemkul at vt.edu
Fri Jul 13 12:24:27 CEST 2012
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
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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