VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 13 2014 - 19:43:21 CST

On Mon, Jan 13, 2014 at 7:27 PM, . Juita <juita_at_uon.edu.au> wrote:
> Dear VMD users,
>
>
>
> I am trying to calculate the RDF from the trajectories files obtained from
> DFTB+ and CPMD simulation. However, the value drops to zero after about 7.2
> A. It does not reach one in long distances. I tried to increase the
> simulation box, but the results still indicate the value of zero after 7.2
> A. The attached is the example of the geometry of the trajectories. I
> would appreciate any assistance for this issue.

two things:
- you cannot specify *any* box, but you have to use *exactly* the box
dimensions that were used during the simulation. since .xyz files do
not contain box information, you have to set it manually for all
frames.
- the measure gofr command applies minimum image conventions, so you
can get the g(r) with maximum accuracy only up to half the smallest
box diameter. the code can go "into the corners" (i.e. up to
sqrt(3)*half the box) but then the statistics get increasingly worse.

for more details, please read up on the measure gofr command in the
VMD user's guide.

axel.

>
>
>
> Many thanks and best regards,
>
> Juita 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.