VMD-L Mailing List

From: Philippe Bopp / temporary (philippebopp_at_yahoo.com)
Date: Mon Dec 03 2012 - 06:56:54 CST

Hi ramin

>I have a problem in analysing of  RDF in VMD by employing dump of lammps.
>I have 2 system
>1.zeolite with one unit cell

 it is cubic, I suppose

>2.Zeolite with 4 unit cell.
 in this case, your simulation box is not cubic,
 the next biggest cubic simulation box after one
 uni cell would contain 8 unit cells

>I analyse the RDF of Al in zeolite to Na ions (Al-Na)
>I expect to have the same results in both system.

 at short dictance more or less (but only more or less)
 yes,

 at larger distances see below

>but I have not . the RDF of Al -Na in  system that include 4
>unit cell is different and more than in one unit cell.

 If you really used 4 uni cells, let's say in x- and y-
 directions, you would have box_x = box_y = 2* box_z
 and you can strictly compute g(r) only up to box_z / 2,
 otherwise some periodic images enter your g(r), or the
 normalization becomes tricky (you'ld have to do it
 manually, not with VMD)

 Why are, as Axel pointed out, the g(r) 'in principle'
 different for different boxsizes? Because in small
 simulation boxes, some 'types' of motion cannot
 occur, namely the ones which are incompatible with
 the small periodicity (in solid state physisc you'ld
 call them small (or low)-k phonons). This being said,
 for small r-values (1st and 2nd neighbor peak) the
 difference should be minor (assuming the tempertures
 of the two runs are the same). If it is not,
 check whether you got
 the periodic boundary conditions,
 the range and
 the resolution
 right in the VMD evaluation,
 and if yes, there is probably a problem with your simulation

 cheers

 Philippe