52
Gromacs can automatically create topology files using the pdb2gmx module, which is a very powerful tool when dealing with
proteins. However, in this case where only heteromolecules are
present in the simulation, the topology file can be created
manually.
1. Create a text file and name it topol.top. A model text file is
available in the online version and presented in Fig. 4. The preferred force field for this simulation is charmm36 [13].
2. Copy the lines presented in Fig. 4 or download the available
topol.top file from the online version.
3. It is very important that the names of the drug molecules in the
last section of topol.top, [molecules], are exactly the same as in
the section [molecule type] of the CC.itp and 2-HP-B-CD.itp
files. If they are not, change them appropriately.
Next step is the creation of the simulation box with the editconf
module. Special care should be taken in order to create a box long
enough, so that the dragged molecule does not interact with the
periodic image of the host molecule.
1. Use the following terminal command:
gmx_d editconf -f complex.gro -o newbox.
gro -center 2.181 2.4775 3.280 -box 6.560
4.362 12
In such a way, a long enough box is created and the complex
is centered at 2.181 2.4775 3.280. The drug molecule will be
pulled along the long dimension at a distance no greater than
half the dimension. This is of great importance since gromacs
calculates distances while taking periodicity into account. If half
of the pulling dimension is exceeded (i.e., 6 nm in this case) the
reference distance becomes the periodic distance which greatly
affects the results.
2. Always check in a visualization software (e.g., VMD [14] where
the simulation box can be visualized) that the complex is oriented appropriately and that the long dimension is aligned with
your pulling direction, as depicted in Fig. 5.
3. In order to recreate Fig. 5 and in case vmd is downloaded and
installed in your workstation, in your working directory press:
vmd newbox.gro
4. In the VMD window press Extensions → Tk Console. In the Tk
Console environment press:
pbc box
and the simulation box will be depicted.
3.1.5 Manually Create
the Topology File
for the Run
3.1.6 Create
the Simulation Box
Sofia Kiriakidi and Thomas Mavromoustakos
Gromacs can automatically create topology files using the pdb2gmx module, which is a very powerful tool when dealing with
proteins. However, in this case where only heteromolecules are
present in the simulation, the topology file can be created
manually.
1. Create a text file and name it topol.top. A model text file is
available in the online version and presented in Fig. 4. The preferred force field for this simulation is charmm36 [13].
2. Copy the lines presented in Fig. 4 or download the available
topol.top file from the online version.
3. It is very important that the names of the drug molecules in the
last section of topol.top, [molecules], are exactly the same as in
the section [molecule type] of the CC.itp and 2-HP-B-CD.itp
files. If they are not, change them appropriately.
Next step is the creation of the simulation box with the editconf
module. Special care should be taken in order to create a box long
enough, so that the dragged molecule does not interact with the
periodic image of the host molecule.
1. Use the following terminal command:
gmx_d editconf -f complex.gro -o newbox.
gro -center 2.181 2.4775 3.280 -box 6.560
4.362 12
In such a way, a long enough box is created and the complex
is centered at 2.181 2.4775 3.280. The drug molecule will be
pulled along the long dimension at a distance no greater than
half the dimension. This is of great importance since gromacs
calculates distances while taking periodicity into account. If half
of the pulling dimension is exceeded (i.e., 6 nm in this case) the
reference distance becomes the periodic distance which greatly
affects the results.
2. Always check in a visualization software (e.g., VMD [14] where
the simulation box can be visualized) that the complex is oriented appropriately and that the long dimension is aligned with
your pulling direction, as depicted in Fig. 5.
3. In order to recreate Fig. 5 and in case vmd is downloaded and
installed in your workstation, in your working directory press:
vmd newbox.gro
4. In the VMD window press Extensions → Tk Console. In the Tk
Console environment press:
pbc box
and the simulation box will be depicted.
3.1.5 Manually Create
the Topology File
for the Run
3.1.6 Create
the Simulation Box
Sofia Kiriakidi and Thomas Mavromoustakos