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

[gaguilar at inescporto.pt]

DEar Dr Hourahine
Thanks for your suggestion, that way (Time Step of 0.1 fs ) works,

best regards,

Gerardo

Quoting Ben Hourahine <benjamin.hourahine at strath.ac.uk>:

> Hello,
>
> 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
> try
>
> 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.
>
> Regards
>
> Ben
>
> 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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>
> --
>      Dr. B. Hourahine, SUPA, Department of Physics,
>    University of Strathclyde, John Anderson Building,
>           107 Rottenrow, Glasgow G4 0NG, UK.
>     +44 141 548 2325, benjamin.hourahine at strath.ac.uk
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