[gmx-users] problem with gmx genconf?

[Thejus Kartha]

Greetings, all.I have been trying to perform a simulation using the following solvent (1,4-dioxane) molecule: 

Screenshot from 2016-10-10 05-11-13.png

  
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Screenshot from 2016-10-10 05-11-13.png
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The .gro file corresponding to this single molecule is as follows:-----------------------------------------------------------------------------------------------------
DIOXANE
    6
  903DOX     CA    1  -8.877   0.470   2.225
  903DOX     CB    2  -9.002   0.499   2.142
  903DOX     CD    3  -9.022   0.274   2.090
  903DOX     CE    4  -8.897   0.244   2.174
  903DOX     OF    5  -9.091   0.387   2.144
  903DOX     OG    6  -8.808   0.357   2.171
   0.28300   0.25490   0.13510----------------------------------------------------------------------------------------------------------
The topology corresponding to this whole operation is as follows:-----------------------------------------------------------------------------------------------------------
;      gmx pdb2gmx -f pdbdio.pdb -o dioxane.gro
;    Force field was read from the standard GROMACS share directory.
;

; Include forcefield parameters
#include "gromos43a1.ff/forcefield.itp"

[ moleculetype ]
; Name            nrexcl
DOX           3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
; residue 903 DOX rtp DOX  q -0.5
     1        CH2    903    DOX     CA      1      0.071     14.027   ; qtot 0.071
     2        CH2    903    DOX     CB      1      0.071     14.027   ; qtot 0.142
     3        CH2    903    DOX     CD      1      0.071     14.027   ; qtot 0.213
     4        CH2    903    DOX     CE      1      0.071     14.027   ; qtot 0.284
     5         OA    903    DOX     OF      1     -0.375    15.9994   ; qtot -0.091
     6         OA    903    DOX     OG      1     -0.375    15.9994   ; qtot -0.466

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     2    gb_14
    1     6     2    gb_12
    2     5     2    gb_12
    3     4     2    gb_14
    3     5     2    gb_12
    4     6     2    gb_12

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     3     1 
    2     4     1 
    5     6     1 

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     6     2    ga_14
    1     2     5     2    ga_14
    4     3     5     2    ga_14
    3     4     6     2    ga_14
    2     5     3     2    ga_9
    1     6     4     2    ga_9

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    6     1     2     5     1    gd_1
    2     1     6     4     1    gd_2
    1     2     5     3     1    gd_2
    5     3     4     6     1    gd_1
    4     3     5     2     1    gd_2
    3     4     6     1     1    gd_2

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "gromos43a1.ff/spce.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "gromos43a1.ff/ions.itp"

[ system ]
; Name
DIOXANE

[ molecules ]
; Compound        #mols
DOX              1--------------------------------------------------------------------------------------------------------
But, when I use the gmx genconf command to expand it into a collection of molecules (8 x 8 x 8 box), the result contains disordered molecules as seen in my VMD window. However, the .gro file produced after the genconf seems to be looking fine though. The genconf generated system looks like this:
Screenshot from 2016-10-10 05-12-09.png
As you can see, the molecules are not seen correctly, that is, there are many places where I have an oxygen in the place of carbon, vice-versa, only carbon containing rings, so on and so forth. Can you please let me know what's going on? I mean, there's no reason why gmx genconf shouldn't be just duplicating the molecule I give it. 

The command I used:
gmx genconf -f dioxane.gro -o diox.gro -nbox 8 8 8 -dist 0.3  -shuffle -rot

  
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Thanks & regards,Thejus Kartha