61
The simulation will take place with a pulling rate of 0.01 nm/ps
(meaning that during the 500 ns of simulation, the drug will be
pulled for 5 nm) and the force constant will be 1000 kl/mol.
1. Create the binary input file using the following command:
gmx_d grompp -f md_pull.mdp –n index.ndx -c
npt.gro -p topol.top -r npt.gro -t npt.cpt -o
pull.tpr
The simulation will be run using a similar command, but in this
case the –px and –pf commands will be used additionally, in order
to save the pull COM coordinates and forces:
gmx_d mdrun -deffnm pull -pf pullf.xvg -px
pullx.xvg
Now a series of configurations will be extracted from the trajectory
in order to use some of them as the starting configuration for the
umbrella sampling procedure, as it is schematically illustrated in
Fig. 3. In order to extract the frames from the pulling trajectory (a
file will have been created and named as pull.xtc), use the trjconv
module of gromacs. When prompted, choose to save the whole
system. The terminal command for the frame extraction is
gmx_d trjconv -s pull.tpr -f pull.xtc -o
conf.gro –sep
A series of coordinate files (conf0.gro, conf1.gro, etc.) will be
produced, corresponding to each of the frames saved in the continuous pulling simulation. The COM distance between CC and
2-HP-B-CD will be calculated by the distance module of gromacs.
To iteratively call the module distance on all of these frames that
were generated, use the bash script (get_distances.sh) provided by
Assist. Prof. Lemkul at his website (http://www.mdtutorials.
com/gmx/umbrella/05_pull.html) and change it as follows. First
comment out or delete the line that starts with “echo 0” since it
contains the command that you just did, i.e., separate the trajectory in frames. Then, alter the number of iterations (for ((i=0;
i<[number of generated conf#.gro here]))) and the name of the
groups (CC and CD in this case). Press the following in the command line:
./get_distances.sh
This script will generate a file named “summary_distances.dat”
with a list of all the conf#.gro files and the corresponding COM
distance of the groups of interest.
In order to select the conf#.gro files that will serve as starting configurations for the umbrella sampling simulation, you need to
decide the COM spacing. Usually a COM spacing of 0.1 nm is
3.4.2 Run the Pulling
Simulation
3.4.3 Collect Frames
3.4.4 Choose
the Starting Configurations
Study of Candesartan Cilexetil: 2-Hydroxypropyl-β-Cyclodextrin Interactions…
The simulation will take place with a pulling rate of 0.01 nm/ps
(meaning that during the 500 ns of simulation, the drug will be
pulled for 5 nm) and the force constant will be 1000 kl/mol.
1. Create the binary input file using the following command:
gmx_d grompp -f md_pull.mdp –n index.ndx -c
npt.gro -p topol.top -r npt.gro -t npt.cpt -o
pull.tpr
The simulation will be run using a similar command, but in this
case the –px and –pf commands will be used additionally, in order
to save the pull COM coordinates and forces:
gmx_d mdrun -deffnm pull -pf pullf.xvg -px
pullx.xvg
Now a series of configurations will be extracted from the trajectory
in order to use some of them as the starting configuration for the
umbrella sampling procedure, as it is schematically illustrated in
Fig. 3. In order to extract the frames from the pulling trajectory (a
file will have been created and named as pull.xtc), use the trjconv
module of gromacs. When prompted, choose to save the whole
system. The terminal command for the frame extraction is
gmx_d trjconv -s pull.tpr -f pull.xtc -o
conf.gro –sep
A series of coordinate files (conf0.gro, conf1.gro, etc.) will be
produced, corresponding to each of the frames saved in the continuous pulling simulation. The COM distance between CC and
2-HP-B-CD will be calculated by the distance module of gromacs.
To iteratively call the module distance on all of these frames that
were generated, use the bash script (get_distances.sh) provided by
Assist. Prof. Lemkul at his website (http://www.mdtutorials.
com/gmx/umbrella/05_pull.html) and change it as follows. First
comment out or delete the line that starts with “echo 0” since it
contains the command that you just did, i.e., separate the trajectory in frames. Then, alter the number of iterations (for ((i=0;
i<[number of generated conf#.gro here]))) and the name of the
groups (CC and CD in this case). Press the following in the command line:
./get_distances.sh
This script will generate a file named “summary_distances.dat”
with a list of all the conf#.gro files and the corresponding COM
distance of the groups of interest.
In order to select the conf#.gro files that will serve as starting configurations for the umbrella sampling simulation, you need to
decide the COM spacing. Usually a COM spacing of 0.1 nm is
3.4.2 Run the Pulling
Simulation
3.4.3 Collect Frames
3.4.4 Choose
the Starting Configurations
Study of Candesartan Cilexetil: 2-Hydroxypropyl-β-Cyclodextrin Interactions…