[gmx-users] building up a long polymer chain

[Moeed]

Hello Justin,

I created structure file for a 4-carbon repeating unit as follows:
HETATM    1  CAA DRG     1      14.260  -4.270   0.000  1.00
20.00             C
HETATM    2 1HAA DRG     1      14.175  -3.426   0.530  1.00
20.00             H
HETATM    3 2HAA DRG     1      15.050  -4.790   0.326  1.00
20.00             H
HETATM    4 3HAA DRG     1      14.385  -4.045  -0.966  1.00
20.00             H
HETATM    5  CAB DRG     1      12.990  -5.110   0.170  1.00
20.00             C
HETATM    6 1HAB DRG     1      12.205  -4.581  -0.153  1.00
20.00             H
HETATM    7 2HAB DRG     1      12.871  -5.326   1.139  1.00
20.00             H
HETATM    8  CAC DRG     1      13.070  -6.410  -0.620  1.00
20.00             C
HETATM    9 1HAC DRG     1      13.855  -6.939  -0.297  1.00
20.00             H
HETATM   10 2HAC DRG     1      13.189  -6.194  -1.589  1.00
20.00             H
HETATM   11  CAD DRG     1      11.800  -7.250  -0.450  1.00
20.00             C
HETATM   12 1HAD DRG     1      11.885  -8.094  -0.980  1.00
20.00             H
HETATM   13 2HAD DRG     1      11.675  -7.475   0.516  1.00
20.00             H
HETATM   14 3HAD DRG     1      11.010  -6.730  -0.776  1.00
20.00             H

I renamed the atoms and removed one hydrogen atoms from both ends to get
repeating unit. CH2CH2,

1- I am not able to produce the repeating unit C2H4 in PRODRG. It adds the
third H automatically. I dont know anyother way but removing the third H
from structure file by hand..

Then I mesaured the C1 To C4 distance which is 0.388 A.

editconf -f prodrg.pdb -o prodrg.gro -box 0.388 -bt cubic

 12
    1DRG     C1    1   0.208   0.006   0.242
    1DRG    H11    2   0.158   0.010   0.328
    1DRG    H12    3   0.149  -0.030   0.170
    1DRG     C2    4   0.255   0.148   0.203
    1DRG    H21    5   0.305   0.143   0.116
    1DRG    H22    6   0.314   0.184   0.274
    1DRG     C3    7   0.133   0.240   0.186
    1DRG    H31    8   0.083   0.245   0.272
    1DRG    H32    9   0.074   0.204   0.114
    1DRG     C4   10   0.179   0.382   0.147
    1DRG    H41   11   0.239   0.418   0.218
    1DRG    H42   12   0.230   0.378   0.060
   0.38800   0.38800   0.38800

then : genconf -f prodrg.gro -o rep.gro -nbox 1 5 1

2- The problem here is that one CH2 unit with 2 H atoms is falling on the
next repeating unit in the next box. i.e 4 H atoms and C atoms are
overlapping... as shown below:

 H H H *H H* H H H
 | |  |  | |  | | |
 C-C-C-*CC*-C-C-C
 | |  |  | | |  |  |
 H H H *H H* H H H

Do you think I should use -d option?

Please guide me..
Thanks
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