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 Christian -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
