[gmx-users] Box size and potential energy calculation
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Jan 22 01:39:57 CET 2011
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
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