[DFTB-Plus-User] Format of the MD run results

Ben Hourahine benjamin.hourahine at strath.ac.uk
Tue Jun 23 10:28:57 CEST 2009


the format is the old xmol xyz, so

Species x y z (then optional:) electrons_atom v_x v_y v_z

with the code outputting in Angstroms, electron charges and Angstroms/ps
for the three types of unit. The number of electrons on each
atom is only present if the run is SCC or uses Mulliken analysis.

The reason your atoms are not moving seems to be that your time step
is 1.0e-15 atomic units, which would be approximately 4*10^-18 s. I'd

TimeStep [s] = 1.0e-15

but this is a bit long for systems containing C-H bonds, I use around

TimeStep [fs] = 0.1

but you should test the effect on your results. The Andersen thermostat
would probably allow a longer time step.



gaguilar at inescporto.pt wrote:
> Hi,
> I was running a MD calculation of a complex system of a peptide and
> several solvents, de resulting .xyz file have seven columns for each
> atom. I think that the first three columns are the initial coordinates
> (and does not change in all the file), but I am unsure about the
> meaning of the last four columns. anybody can help me?
> Other question if the first three columns are the final coordinates,
> why they does not change? Attached is my input file.
> thanks in advance,
> Gerardo González Aguilar
> Senior Researcher
> INESC-Porto
> Portugal
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