[gmx-users] Box size and potential energy calculation

Christian Mötzing christian at moetzing.net
Sat Jan 22 16:36:45 CET 2011

Am Samstag, den 22.01.2011, 11:39 +1100 schrieb 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.

Ok and where do the box vectors come from? I read the a atom/molecule
has a vector for the position and a vector for the velocity/direction
its heading. Are the box vectors determined by the vectors which have
the maximal component for one axis in the system?

> > 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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