[gmx-users] Box size and potential energy calculation
christian at moetzing.net
Sun Jan 23 12:58:38 CET 2011
Am Sonntag, den 23.01.2011, 09:40 +1100 schrieb Mark Abraham:
> On 23/01/2011 2:36 AM, Christian Mötzing wrote:
> > 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?
> The size of the box, if any, is imposed by the user before the
> simulation begins (e.g with editconf). It may have periodic boundary
> conditions. Its size may vary if the simulation is not in a
> constant-volume ensemble.
For the waterbox simulation I got the box size does vary over time. PBC
is also used. It is important for me to know whether the box size
depends on the position of the molecules or whether the box size is
calculated by the force the molecules create when bumping on the virtual
wall of the box. If you can point me to some literature where this is
explained I would be really happy. :)
> It sounds like doing some tutorial material would give you some good
> context in which to continue learning.
> >>> 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
> > Christian
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