@@ -127,8 +127,8 @@ Again, the files created will be called ``36KB_length.dat`` and ``36KB_angle.dat
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@@ -127,8 +127,8 @@ Again, the files created will be called ``36KB_length.dat`` and ``36KB_angle.dat
These samples were compared in the paper using an R script to generate a series of boxplots, but a simpler Python script is provided which may be used to compare the mean and standard deviations of the samples::
These samples were compared in the paper using an R script to generate a series of boxplots, but a simpler Python script is provided which may be used to compare the mean and standard deviations of the samples::
If the automatically generated parameters provide an accurate representation of the reference structure, the percentage error between the two samples will be small.
If the automatically generated parameters provide an accurate representation of the reference structure, the percentage error between the two samples will be small.
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@@ -141,7 +141,7 @@ This may be performed using the standard GROMACS too `gmx gyrate`::
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@@ -141,7 +141,7 @@ This may be performed using the standard GROMACS too `gmx gyrate`::
These commands will calculate the radius of gyration for each trajectory frame for both the reference and CG simulations.
These commands will calculate the radius of gyration for each trajectory frame for both the reference and CG simulations.
The resulting `.xvg` files may be visualised using a graphing program such as `xmgrace` or compared in the same way as the bonded samples, using::
The resulting `.xvg` files may be visualised using a graphing program such as `xmgrace` or compared in the same way as the bonded samples, using::
average_columns.py ref-gyr.xvg cg-gyr.xvg
./average_columns.py ref-gyr.xvg cg-gyr.xvg
As before, a small percentage difference in each of the columns suggests good replication of gross conformation.
As before, a small percentage difference in each of the columns suggests good replication of gross conformation.