55
1. The terminal command is the following:
gmx_d mdrun –s em.tpr -deffnm em
The above option should be altered if it is run on a supercomputing system using several processors in parallel by using
the gmx_d_mpi command instead.
The system will be first equilibrated in the canonical ensemble
under constant volume and temperature.
The input for the dynamics simulation will be created in a similar
fashion as described before for the minimization process. The
module grompp will be called and it will produce a binary input file
(nvt.tpr) after reading the relevant protocol file (nvt.mdp). An
example NVT equilibration protocol is available in the online version and presented in Fig. 7.
First, create an index file where you will group the 2-HP-B and CC
molecules together. In the terminal press:
gmx_d make_ndx –f em.gro –o index.ndx
Press the numbers of the molecules you want to group together
by pressing, e.g.,
2 | 3
If 2-HP-B-CD is 2 and CC is 3, then press q. In case the species at your system are numbered differently, choose the appropriate number to group CC and 2-HP-B-CD together.
3.3 Equilibration
3.3.1 NVT Ensemble
Equilibration
Create Input
Create Input
Fig. 6 A model protocol file for the energy minimization process
Study of Candesartan Cilexetil: 2-Hydroxypropyl-β-Cyclodextrin Interactions…
1. The terminal command is the following:
gmx_d mdrun –s em.tpr -deffnm em
The above option should be altered if it is run on a supercomputing system using several processors in parallel by using
the gmx_d_mpi command instead.
The system will be first equilibrated in the canonical ensemble
under constant volume and temperature.
The input for the dynamics simulation will be created in a similar
fashion as described before for the minimization process. The
module grompp will be called and it will produce a binary input file
(nvt.tpr) after reading the relevant protocol file (nvt.mdp). An
example NVT equilibration protocol is available in the online version and presented in Fig. 7.
First, create an index file where you will group the 2-HP-B and CC
molecules together. In the terminal press:
gmx_d make_ndx –f em.gro –o index.ndx
Press the numbers of the molecules you want to group together
by pressing, e.g.,
2 | 3
If 2-HP-B-CD is 2 and CC is 3, then press q. In case the species at your system are numbered differently, choose the appropriate number to group CC and 2-HP-B-CD together.
3.3 Equilibration
3.3.1 NVT Ensemble
Equilibration
Create Input
Create Input
Fig. 6 A model protocol file for the energy minimization process
Study of Candesartan Cilexetil: 2-Hydroxypropyl-β-Cyclodextrin Interactions…