57
In a similar way, call the mdrun module of gromacs in order to run
the simulation using the following command:
gmx_d mdrun –s nvt.tpr -deffnm nvt
Upon the completion of the NVT equilibration, the system will be
further equilibrated in the isothermal-isobaric ensemble, i.e., under
constant pressure and temperature. The procedure is similar as discussed for the canonical example but different equilibration protocols will be used. The NPT equilibration protocol is available in the
online version and presented in Fig. 8.
The terminal command to be used in order to produce the binary
input file in accordance with the minimization protocol is the
following:
gmx_d grompp -f npt.mdp –n index.ndx -c nvt.
gro –r nvt.gro -p topol.top -o npt.tpr
Run the simulation using the following command:
gmx_d mdrun –s npt.tpr -deffnm npt
The next step after having properly equilibrated the system is to
perform the sMD simulation. The CC molecule will be pulled out
of the 2-HP-B-CD’s cavity, by applying an external potential that
perturbs the system’s Hamiltonian as described previously.
It is very important to create a pulling protocol that reflects the
specific pulling action that is intended. Special care should be taken
in order to select the direction of your reaction coordinate. In this
specific case, we will pull the drug molecule along the z-direction
which is aligned with the cavity’s opening as illustrated in Fig. 9.
The pulling protocol is available in the online version and presented in Fig. 10. The total pulling simulation will be 500 ps and
snapshots will be saved every 1 ps. Although the protocol files are
commented with self-explanatory comments and most of it is similar to the protocols discussed below, some of its parts will be discussed further. In particular, the section that is responsible for the
pulling is the following:
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one
reaction coordinate
pull_group1_name = CC
Run the Equilibration
Simulation
3.3.2 NPT Ensemble
Equilibration
Create Input
Run the Equilibration
Simulation
3.4 Steered
Molecular Dynamics
Simulation
3.4.1 Create Input
for the Pulling Simulation
Study of Candesartan Cilexetil: 2-Hydroxypropyl-β-Cyclodextrin Interactions…
In a similar way, call the mdrun module of gromacs in order to run
the simulation using the following command:
gmx_d mdrun –s nvt.tpr -deffnm nvt
Upon the completion of the NVT equilibration, the system will be
further equilibrated in the isothermal-isobaric ensemble, i.e., under
constant pressure and temperature. The procedure is similar as discussed for the canonical example but different equilibration protocols will be used. The NPT equilibration protocol is available in the
online version and presented in Fig. 8.
The terminal command to be used in order to produce the binary
input file in accordance with the minimization protocol is the
following:
gmx_d grompp -f npt.mdp –n index.ndx -c nvt.
gro –r nvt.gro -p topol.top -o npt.tpr
Run the simulation using the following command:
gmx_d mdrun –s npt.tpr -deffnm npt
The next step after having properly equilibrated the system is to
perform the sMD simulation. The CC molecule will be pulled out
of the 2-HP-B-CD’s cavity, by applying an external potential that
perturbs the system’s Hamiltonian as described previously.
It is very important to create a pulling protocol that reflects the
specific pulling action that is intended. Special care should be taken
in order to select the direction of your reaction coordinate. In this
specific case, we will pull the drug molecule along the z-direction
which is aligned with the cavity’s opening as illustrated in Fig. 9.
The pulling protocol is available in the online version and presented in Fig. 10. The total pulling simulation will be 500 ps and
snapshots will be saved every 1 ps. Although the protocol files are
commented with self-explanatory comments and most of it is similar to the protocols discussed below, some of its parts will be discussed further. In particular, the section that is responsible for the
pulling is the following:
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one
reaction coordinate
pull_group1_name = CC
Run the Equilibration
Simulation
3.3.2 NPT Ensemble
Equilibration
Create Input
Run the Equilibration
Simulation
3.4 Steered
Molecular Dynamics
Simulation
3.4.1 Create Input
for the Pulling Simulation
Study of Candesartan Cilexetil: 2-Hydroxypropyl-β-Cyclodextrin Interactions…