Isotopic dilution study

Eric Shamay eric.... at gmail.com
Tue Dec 2 20:43:53 CET 2008


Teo,

thanks for your help on this. I've just output the first 1000
timesteps and verified that the system is doing what it should be
doing, and convinced myself that even though the output says H, it's
still behaving like a D. I just generated some IR data from the system
dipole autocorrelation function and the spectra look convincing.

thanks a lot!

~Eric



On Dec 1, 10:54 pm, Laino Teodoro <teodor... at gmail.com> wrote:
> Hi Eric,
>
> On 2 Dec 2008, at 01:46, Eric Shamay wrote:
>
>
>
> > One last issue on this - When the trajectories are printed (i.e. when
> > doing geo_opt or MD) the output XYZ file contains the name of the
> > element H again. I.e. my input coordinates specify that the atom name
> > is 'D', but then the output, instead of printing 'D' for each atom, it
> > prints out 'H' as if I had never changed the KIND. Is the output based
>
> of course you never changed the KIND, but the "standard" of XYZ is to
> have:
>
> ELEMENT X Y Z
>
> and not
>
> KIND x y z
>
> If you want to be able to track the "D", then I suggest you to  
> exploit the
> capabilities of VMD, first loading an XYZ with the names you like and  
> loading
> on the top of that molecule the whole trajectory you like (since the  
> order of the atoms
>   in the trajectory is the same as the one in input).
> Instead of the original XYZ, you can as well use PSF or PDB.
>
> Teo
>


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