Hongyan Xiao wrote:
Hi,
I has used the periodic boundary conditions and correct em.mdp
file. However, the minimized result is water/decane/water, while I set
decane/water/decane as the initial system . I cannot understand the
reason. Please give me some constructive suggestion! Thanks!
You need to understand that decane/water/decane under periodic boundary
conditions has only one interface... the two decane segments are
contiguous. Further, there's nothing magical about where you've placed
that interface with respect to your initial box, since there are an
infinite number of mathematically equivalent alternatives. The physics
of the system and the algorithms in GROMACS will feel free to ignore
your arbitrary choice. If you want to reconstruct a particular choice
after a simulation, you will need to play around with editconf and/or
trjconv.
Mark
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