62
adequate, but in case needed, more configurations can be added
later. Open the summary_distances.dat file and make note of the
number of each conf#.gro file that is separated by 0.1 nm. In this
way, you will create a list of 40–50 starting configurations, depending on your system. There is no need to be extremely precise with
the spacing. What is important is to have a good overlap between
the separate windows (i.e., the independent simulations for the
umbrella sampling procedure), as it will be explained more thoroughly in the next sections. Only after completing the umbrella
sampling simulations will you be able to check if the overlap is
adequate, so at first a guess on the spacing must be made.
Before proceeding with the separate unbiased MD simulations, a
short equilibration will take place for each of the starting configurations. If the chosen starting configurations were, e.g., the following (the numbers are just indicative):
1. conf0.gro
2. conf10.gro
3. conf31.gro
4. conf80.gro
…
50. conf500.gro
the grompp module will be used in order to create 50 binary
input files for the NPT equilibration of each of the starting windows. Note that these conf#.gro files are indicative and in your
simulation might differ, because they depend on the exact pose of
the drug molecule inside 2-HP-B-CD’s cavity. The NPT equilibration protocol is available in the online version and presented in
Fig. 11.
1. The terminal command for creating the equilibration input is
the following:
gmx_d grompp -f npt_umbrella.mdp -c conf0.
gro -p topol.top -r conf0.gro -n index.ndx -o
npt1.tpr
...
gmx_d grompp -f npt_umbrella.mdp -c conf500.
gro -p topol.top -r conf500.gro -n index.
ndx -o npt50.tpr
2. Then, each equilibration simulation should be run independently using the mdrun module as follows:
gmx_d mdrun -deffnm npt1
...
gmx_d mdrun -deffnm npt50
3.5 Umbrella
Sampling
3.5.1 Equilibration
Sofia Kiriakidi and Thomas Mavromoustakos
adequate, but in case needed, more configurations can be added
later. Open the summary_distances.dat file and make note of the
number of each conf#.gro file that is separated by 0.1 nm. In this
way, you will create a list of 40–50 starting configurations, depending on your system. There is no need to be extremely precise with
the spacing. What is important is to have a good overlap between
the separate windows (i.e., the independent simulations for the
umbrella sampling procedure), as it will be explained more thoroughly in the next sections. Only after completing the umbrella
sampling simulations will you be able to check if the overlap is
adequate, so at first a guess on the spacing must be made.
Before proceeding with the separate unbiased MD simulations, a
short equilibration will take place for each of the starting configurations. If the chosen starting configurations were, e.g., the following (the numbers are just indicative):
1. conf0.gro
2. conf10.gro
3. conf31.gro
4. conf80.gro
…
50. conf500.gro
the grompp module will be used in order to create 50 binary
input files for the NPT equilibration of each of the starting windows. Note that these conf#.gro files are indicative and in your
simulation might differ, because they depend on the exact pose of
the drug molecule inside 2-HP-B-CD’s cavity. The NPT equilibration protocol is available in the online version and presented in
Fig. 11.
1. The terminal command for creating the equilibration input is
the following:
gmx_d grompp -f npt_umbrella.mdp -c conf0.
gro -p topol.top -r conf0.gro -n index.ndx -o
npt1.tpr
...
gmx_d grompp -f npt_umbrella.mdp -c conf500.
gro -p topol.top -r conf500.gro -n index.
ndx -o npt50.tpr
2. Then, each equilibration simulation should be run independently using the mdrun module as follows:
gmx_d mdrun -deffnm npt1
...
gmx_d mdrun -deffnm npt50
3.5 Umbrella
Sampling
3.5.1 Equilibration
Sofia Kiriakidi and Thomas Mavromoustakos