[CPMD-list] Summary MD on a molecule

[Martijn Zwijnenburg]

Hi,

Herewith the answers I got on my question regarding MD on a 
single molecule. Thanx to Jan-Willem Handgraaf and Carme Rovira 
for their answers.

cheers 

Martijn

On 11 Apr 2002, at 18:41, Jan-Willem Handgraaf wrote:

> If you use the option "SYMMETRY 0" you automatically also turn 
on the option 
> "ISOLATED MOLECULE". Now if you choose another symmetry 
and also the 
> "ISOLATED MOLECULE" option you can study an isolated 
molecule or cluster 
> within periodic boundary conditions. And if you choose your box 
big enough 
> the "CENTER MOLECULE" option is rather arbitrary, assuming 
that you start the 
> simulation with the molecule in the center of you box.
> It all depends on the question if you want the molecules to 'feel 
each other' 
> or not? If yes, use the correct periodic symmetry of the system 
with the 
> "ISOLATED MOLECULE" option, if not "SYMMETRY 0" will 
suffice. This latter 
> option is more expensive, because the program uses a scheme 
to correct for 
> the periodic images (i.e. Hockney) which in principle should not be 
there.
> 
> Jan-Willem Handgraaf
> 
> 
> -- 
> Jan-Willem Handgraaf
> Department of Chemical Engineering
> University of Amsterdam
> Nieuwe Achtergracht 166
> 1018 WV Amsterdam
> The Netherlands
> 
> Room: C6.18
> Tel: +31-20-5256492
> Fax: +31-20-5255604
> Email: jwh at science.uva.nl

On 11 Apr 2002, at 19:44, Carme Rovira wrote:

> Hello,
> 
> I send you an input example for an isolated
> water molecule in an isolated box (h2o_pbc.inp).
> Alternatively you can also run it in a non-periodic
> box (see h2o_isolated.inp) using together 
> ISOLATED MOLECULE and 0 for SYMMETRY.
> 
> In general, the computed properties of the molecule 
> should be independent of the scheme used (either pbc or isolated
> box) except in difficult cases such as charged molecules, 
> where the calculation in an isolated box is recommended.
> The PBC calculation is always cheaper so for
> a neutral molecule such as water molecule you would
> save time and memory.
> 
> In the case of a calculation in an isolated box, CPMD moves
> the center of mass to the center of the box by default,
> unless you use the keywords (CENTER MOLECULE OFF). I 
would
> just use the default in your case.
> 
> Good luck!
> 
> Carme
> 
> 
====================================================
=====================
> Carme Rovira
> Centre de Química Teòrica            Tel: +34 93 4037112
> Parc Científic de Barcelona          Fax: +34 93 4037225
> Josep Samitier 1-5 Annex A. Pta 1    E-mail: crovira at pcb.ub.es
> 08028 Barcelona, Spain               (http://www.pcb.ub.es)
> ----------- and ------------
> Departament de Química Física
> Facultat de Química. Universitat de Barcelona
> Martí i Franquès 1. 08028 Barcelona. Spain
> (http://www.qf.ub.es/personal/crovira)
> 
====================================================
=====================
> 
> 
-------------------------------------------------------------------------
Martijn Zwijnenburg
Lab. of Applied Organic Chemistry and Catalysis
Delft University of Technology
Julianalaan 136
2628 BL Delft
The Netherlands
Tel: 0031-(0)152782691
Fax: 0031-(0)152784700
e-mail: M.A.Zwijnenburg at tnw.tudelft.nl
web page: http://come.to/tock