Tutorial clarifications
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@@ -12,7 +12,7 @@ Atomistic Simulation
@@ -12,7 +12,7 @@ Atomistic Simulation
The reference simulation for the parametrisation of atenolol was performed using the GROMOS 54A7 united atom forcefield with a topology from the `ATB database <https://atb.uq.edu.au/molecule.py?molid=23433>`_.
A single molecule of atenolol was solvated and equilibrated, before collecting a 50 ns trajectory using the GROMACS molecular dynamics simulator.
A reduced copy of this trajectory is provided in the tutorial files since the original is prohibitively large.
@@ -72,7 +72,7 @@ Model Generation
@@ -72,7 +72,7 @@ Model Generation
The process of model generation after having created the mapping and bond definition files is automated by PyCGTOOL.
In the simplest case, a parameter set may be generated simply by passing the four input files to PyCGTOOL::
This will create two output files ``out.gro``, the mapped CG coordinates, and ``out.itp``, the calculated CG model parameters.
@@ -86,7 +86,8 @@ The output coordinates ``out.gro`` must be solvated using the GROMACS tool `gmx
@@ -86,7 +86,8 @@ The output coordinates ``out.gro`` must be solvated using the GROMACS tool `gmx
Add the line "W 251" to the bottom of the `.top` file, since 251 should be the number of water molecules added by `gmx solvate`.
@@ -110,7 +111,7 @@ Additionally, other methods of validation should be applied relevant to the clas
@@ -110,7 +111,7 @@ Additionally, other methods of validation should be applied relevant to the clas
To compare the distribution of bonded terms, we must first rerun PyCGTOOL to generate samples of the bonded measurements.
In the menu, set the advanced option `dump_measurements` to `True` by selecting it with the arrow keys and toggling with the enter key.
@@ -126,8 +127,8 @@ Again, the files created will be called ``36KB_length.dat`` and ``36KB_angle.dat
@@ -126,8 +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::
If the automatically generated parameters provide an accurate representation of the reference structure, the percentage error between the two samples will be small.
@@ -137,10 +138,11 @@ This may be performed using the standard GROMACS too `gmx gyrate`::
@@ -137,10 +138,11 @@ 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.
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::
As before, a small percentage difference in each of the columns suggests good replication of gross conformation.