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.<br>
<br>
-<br>
Karamyog.<br>
<br>
here are my .top and .gro files.<br>
<br>
conf.gro :- <br>
<br>
DILUTE OXYGEN GAS<br>
27<br>
1MY OX 1 0.010000 0.022000 -0.10000 ; 0.000 0.000 0.000<br>
2MY OX 2 0.250000 0.000000 0.000000 ; 0.000 0.000 0.000<br>
3MY OX 3 0.000000 0.250000 0.000000 ; 0.000 0.000 0.000<br>
4MY OX 4 0.000000 0.000000 0.250000 ; 0.000 0.000 0.000<br>
5MY OX 5 0.250000 0.250000 0.000000 ; 0.000 0.000 0.000<br>
6MY OX 6 0.250000 0.000000 0.250000 ; 0.000 0.000 0.000<br>
7MY OX 7 0.000000 0.250000 0.250000 ; 0.000 0.000 0.000<br>
8MY OX 8 0.250000 0.250000 0.250000 ; 0.000 0.000 0.000<br>
9MY OX 9 0.500000 0.000000 0.000000 ; 0.000 0.000 0.000<br>
10MY OX 10 0.000000 0.500000 0.000000 ; 0.000 0.000 0.000<br>
11MY OX 11 0.000000 0.000000 0.500000 ; 0.000 0.000 0.000<br>
12MY OX 12 0.500000 0.500000 0.000000 ; 0.000 0.000 0.000<br>
13MY OX 13 0.500000 0.000000 0.500000 ; 0.000 0.000 0.000<br>
14MY OX 14 0.000000 0.500000 0.500000 ; 0.000 0.000 0.000<br>
15MY OX 15 0.500000 0.500000 0.500000 ; 0.000 0.000 0.000<br>
16MY OX 16 0.500000 0.250000 0.000000 ; 0.000 0.000 0.000<br>
17MY OX 17 0.500000 0.250000 0.250000 ; 0.000 0.000 0.000<br>
18MY OX 18 0.500000 0.250000 0.500000 ; 0.000 0.000 0.000<br>
19MY OX 19 0.500000 0.500000 0.250000 ; 0.000 0.000 0.000<br>
20MY OX 20 0.250000 0.500000 0.000000 ; 0.000 0.000 0.000<br>
21MY OX 21 0.250000 0.500000 0.250000 ; 0.000 0.000 0.000<br>
22MY OX 22 0.250000 0.500000 0.500000 ; 0.000 0.000 0.000<br>
23MY OX 23 0.250000 0.000000 0.500000 ; 0.000 0.000 0.000<br>
24MY OX 24 0.250000 0.250000 0.500000 ; 0.000 0.000 0.000<br>
25MY OX 25 0.500000 0.000000 0.250000 ; 0.000 0.000 0.000<br>
26MY OX 26 0.000000 0.500000 0.250000 ; 0.000 0.000 0.000<br>
27MY OX 27 0.000000 0.250000 0.500000 ; 0.000 0.000 0.000<br>
0.5 0.5 0.5<br>
<br>
<br>
topol.top :-<br>
#include "ffG53a6.itp"<br>
#include "ffgmx.itp"<br>
<br>
[ moleculetype ]<br>
Ions 1<br>
<br>
[ atoms ]<br>
1 OX
1 MY
OX 0
-0.450 15.99940<br>
<br>
[ system ]<br>
dilute oxygen<br>
[ molecules ]<br>
Ions 27<br>
<br>
<br>
<br>