[gmx-users] Box size and potential energy calculation

Christian Mötzing christian at moetzing.net
Thu Jan 20 20:47:34 CET 2011


I currently read through the GMX manual 4.5.3. I have two questions:

1) Density is calculated by the density of the material and the box
volume. But I can't find a reference on how the box size is calculated.
Can you point me to some literature?

2) I wanted to look up the calculation of the potential energy. Do I
understand the calculation correctly:
- pairwise sum over all molecules
- for each pair Coulomb, Lennard-Jones and bonded terms are summed
- the calculation involves the position of the molecules (for example



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