[gmx-users] Replicating monomer units

[Moeed]

Hello Justin,

I spent a full day to find a proper value for -d but it seems there is no
way of getting  correct bond lenght and angle at the same time. With the
following commands I am getting correct bond length for the atoms connecting
two monomer units but the angle is 140. I get 110 angle only when bond
distance is much less than actual value (1.53 A). I have also tried monomer
units with 6, 8, 10 carbon atoms. For 8 and 10 cases I can not even align
carbons with the axis using princ. This proper geometry problem seems to be
a very simple thing to figure out but I have reached no results. I would
like you to provide me with a hint or suggestion...I appreciate your help.
Thanks.

Great Red Owns Many ACres of Sand
    4
    1Eth     C1    1   0.462   0.285   0.269
    1Eth     C2    2   0.325   0.216   0.269
    1Eth     C3    3   0.213   0.321   0.269
    1Eth     C4    4   0.075   0.255   0.269
   0.53817   0.53817   0.53817

editconf -f 4C.pdb -o 4Cd-princ.gro -princ -d 0.075 -bt cubic
genconf -f 4Cd-princ.gro -o 4Cd-rep.gro -nbox 5 1 1

4Cd-rep.gro: replicated units:

Great Red Owns Many ACres of Sand
   20
    1Eth     C1    1   0.462   0.285   0.269  0.0000  0.0000  0.0000
    1Eth     C2    2   0.325   0.216   0.269  0.0000  0.0000  0.0000
    1Eth     C3    3   0.213   0.321   0.269  0.0000  0.0000  0.0000
    1Eth     C4    4   0.075   0.255   0.269  0.0000  0.0000  0.0000
    2Eth     C1    5   1.000   0.285   0.269  0.0000  0.0000  0.0000
    2Eth     C2    6   0.863   0.216   0.269  0.0000  0.0000  0.0000
    2Eth     C3    7   0.751   0.321   0.269  0.0000  0.0000  0.0000
    2Eth     C4    8   0.613   0.255   0.269  0.0000  0.0000  0.0000
    3Eth     C1    9   1.538   0.285   0.269  0.0000  0.0000  0.0000
    3Eth     C2   10   1.401   0.216   0.269  0.0000  0.0000  0.0000
    3Eth     C3   11   1.289   0.321   0.269  0.0000  0.0000  0.0000
    3Eth     C4   12   1.151   0.255   0.269  0.0000  0.0000  0.0000
    4Eth     C1   13   2.077   0.285   0.269  0.0000  0.0000  0.0000
    4Eth     C2   14   1.940   0.216   0.269  0.0000  0.0000  0.0000
    4Eth     C3   15   1.828   0.321   0.269  0.0000  0.0000  0.0000
    4Eth     C4   16   1.690   0.255   0.269  0.0000  0.0000  0.0000
    5Eth     C1   17   2.615   0.285   0.269  0.0000  0.0000  0.0000
    5Eth     C2   18   2.478   0.216   0.269  0.0000  0.0000  0.0000
    5Eth     C3   19   2.366   0.321   0.269  0.0000  0.0000  0.0000
    5Eth     C4   20   2.228   0.255   0.269  0.0000  0.0000  0.0000
   2.69085   0.53817   0.53817
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