[gmx-users] Box size and potential energy calculation

[Mark Abraham]

On 21/01/2011 6:47 AM, Christian Mötzing wrote:
> Hi,
>
> 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?

The volume of the box is the determinant of the matrix formed by the box 
vectors. If that matrix is upper- or lower-triangular, then the volume 
is the product of the entries in the leading diagonal.

> 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
> aswell
> - the calculation involves the position of the molecules (for example
> Lennard-Jones)

Well that's vaguely accurate. Bonded terms can involve more than pairs 
of atoms.

Mark