[gmx-users] Ngmx

[karamyog singh]

Respected gentlemen, I have written another code for simulating atomic
oxygen. the code is running fine. however when i view my run using ngmx, the
entire box doesn't get filled up.It just shows one plane of atoms. I have a
box of 27 atoms but ngmx shows only 9. Can any1 tell me why and the solution
to this problem.

-
Karamyog.

here are my .top and .gro files.

conf.gro :-

DILUTE OXYGEN GAS
 27
  1MY   OX    1  0.010000   0.022000  -0.10000 ; 0.000 0.000 0.000
  2MY   OX    2  0.250000   0.000000  0.000000 ; 0.000 0.000 0.000
  3MY   OX    3  0.000000   0.250000  0.000000 ; 0.000 0.000 0.000
  4MY   OX    4  0.000000   0.000000  0.250000 ; 0.000 0.000 0.000
  5MY   OX    5  0.250000   0.250000  0.000000 ; 0.000 0.000 0.000
  6MY   OX    6  0.250000   0.000000  0.250000 ; 0.000 0.000 0.000
  7MY   OX    7  0.000000   0.250000  0.250000 ; 0.000 0.000 0.000
  8MY   OX    8  0.250000   0.250000  0.250000 ; 0.000 0.000 0.000
  9MY   OX    9  0.500000   0.000000  0.000000 ; 0.000 0.000 0.000
 10MY   OX   10  0.000000   0.500000  0.000000 ; 0.000 0.000 0.000
 11MY   OX   11  0.000000   0.000000  0.500000 ; 0.000 0.000 0.000
 12MY   OX   12  0.500000   0.500000  0.000000 ; 0.000 0.000 0.000
 13MY   OX   13  0.500000   0.000000  0.500000 ; 0.000 0.000 0.000
 14MY   OX   14  0.000000   0.500000  0.500000 ; 0.000 0.000 0.000
 15MY   OX   15  0.500000   0.500000  0.500000 ; 0.000 0.000 0.000
 16MY   OX   16  0.500000   0.250000  0.000000 ; 0.000 0.000 0.000
 17MY   OX   17  0.500000   0.250000  0.250000 ; 0.000 0.000 0.000
 18MY   OX   18  0.500000   0.250000  0.500000 ; 0.000 0.000 0.000
 19MY   OX   19  0.500000   0.500000  0.250000 ; 0.000 0.000 0.000
 20MY   OX   20  0.250000   0.500000  0.000000 ; 0.000 0.000 0.000
 21MY   OX   21  0.250000   0.500000  0.250000 ; 0.000 0.000 0.000
 22MY   OX   22  0.250000   0.500000  0.500000 ; 0.000 0.000 0.000
 23MY   OX   23  0.250000   0.000000  0.500000 ; 0.000 0.000 0.000
 24MY   OX   24  0.250000   0.250000  0.500000 ; 0.000 0.000 0.000
 25MY   OX   25  0.500000   0.000000  0.250000 ; 0.000 0.000 0.000
 26MY   OX   26  0.000000   0.500000  0.250000 ; 0.000 0.000 0.000
 27MY   OX   27  0.000000   0.250000  0.500000 ; 0.000 0.000 0.000
0.5 0.5 0.5


topol.top :-
#include "ffG53a6.itp"
#include "ffgmx.itp"

[ moleculetype ]
 Ions    1

[ atoms ]
     1          OX      1    MY     OX     0      -0.450    15.99940

[ system ]
dilute oxygen
[ molecules ]
Ions 27
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