[gmx-users] keep the nanotube cylindrical.

[Za Pour]

Dear gmx users
I am simulation a system including carbon nanotube+water.I have done these things:
1. I copied oplsaa.ff folder in my working directory
2. I added following lines to atomname2type.n2t
C    opls_995    0      12.011  2    C  0.142  C 0.142
C    opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
C    opls_997    0      12.011  1    C  0.142  
3.I added these to ffbonded.itp
[ bondtypes ]
 C   C  1   0.1418   478900

 [ angletypes ]
 C   C   C   1  120.000  562.2

[ dihedraltypes ]
 C   C   1   0.000 167.360  1
4.I added these to ffnonbonded.itp
 opls_995   C      6    12.01100     0.000       A    3.85100e-01  4.39600e-01
 opls_996   C      6    12.01100     0.000       A    3.85100e-01  4.39600e-01
 opls_997   C      6    12.01100     0.000       A    3.85100e-01  4.39600e-01
 5.then I run g_x2top with this command:
g_x2top -f cnt.pdb -o cnt.top -name CNT -nexcl 3 -kb 478900 -kt 562.2
6.then I used editconf and genbox:
editconf -f cnt.pdb -o cnt.gro -d 1 -bt cubic
genbox -cp cnt.gro -cs spc216.gro -o sol.gro -p cnt.top
7.I run grompp for EM with this command:
grompp -f em.mdp -c sol.gro -p cnt.top -o em.tpr -maxwarn 1
mdrun -deffnm em
8.again I run grompp for equilibration phase:
grompp -f nvt.mdp -c em.gro -p cnt.top -o nvt.tpr -n index.ndx -maxwarn 1
mdrun -deffnm nvt
However as I looked into the nvt.gro I realized that the cylindrical shape of carbon nanotube
 has been changed.I am not sure what I have done is correct or not?and how to keep nanotube cylindrical ? any help would be really appreciated.
      Best regards
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