69
gmx_d genion -s ions.tpr -o solv_ions.gro -p
topol.top -pname NA -nname CL -neutral -conc
0.115
The -pname option defines the type of the cation which in
this case is sodium (Na) while the –nname option defines the
type of the anion which in this case is chlorine (Cl). Option –
neutral asks genion to place ions until the system is neutralized
while –conc defines the additional salt concentration where in
this case the physiological salt concentration of 0.115 was chosen. After having completed the ion placement, continue with
the energy minimization but in the terminal command, change
solv.gro with solv_ions.gro as follows:
gmx_d grompp -f em.mdp -c solv_ions.gro -p
topol.top -o em.tpr
5. Each force field requires different parametrization in the relevant protocol file. For further details you may visit the gromacs
manual
at
http://www.gromacs.org/Documentation/
Terminology/Force_Fields/CHARMM.
6. Depending on the reaction coordinate you wish to study, you
might want to pull a group of your system in different ways.
The alternatives provided in the gromacs pull code are position,
direction, and direction-periodic. For further details and more
thorough theoretical background visit gromacs manual at
http://manual.gromacs.org/documentation/2019-rc1/
reference- manual/special/pulling.html.
Acknowledgments
Special acknowledgment should be given to Assistant Prof. Justin
Lemkul for providing the comprehensive umbrella sampling tutorial available at www.mdtutorials.com/gmx/umbrella/index.html.
Special thanks to Mrs. Eleni Chontzopoulou for the extensive
tests to the comprehensibility of this protocol. This work was supported by the Hellenic Foundation for Research and Innovation
(HFRI) and the General Secretariat for Research and Technology
(GSRT), under the HFRI PhD Fellowship grant (GA. no. 14551).
The molecular dynamics simulations of this research work were
supported by computational time granted from the Greek Research
and Technology Network (GRNET) in the National HPC facility—ARIS—under project ID MDAT1R and from the ARIS
VI-SEEM HPC facility—under project ID AT1R. The research
leading to these results has been co-funded by the European
Commission under the H2020 Research Infrastructures contract
no. 675121 (project VI-SEEM).
Study of Candesartan Cilexetil: 2-Hydroxypropyl-β-Cyclodextrin Interactions…
gmx_d genion -s ions.tpr -o solv_ions.gro -p
topol.top -pname NA -nname CL -neutral -conc
0.115
The -pname option defines the type of the cation which in
this case is sodium (Na) while the –nname option defines the
type of the anion which in this case is chlorine (Cl). Option –
neutral asks genion to place ions until the system is neutralized
while –conc defines the additional salt concentration where in
this case the physiological salt concentration of 0.115 was chosen. After having completed the ion placement, continue with
the energy minimization but in the terminal command, change
solv.gro with solv_ions.gro as follows:
gmx_d grompp -f em.mdp -c solv_ions.gro -p
topol.top -o em.tpr
5. Each force field requires different parametrization in the relevant protocol file. For further details you may visit the gromacs
manual
at
http://www.gromacs.org/Documentation/
Terminology/Force_Fields/CHARMM.
6. Depending on the reaction coordinate you wish to study, you
might want to pull a group of your system in different ways.
The alternatives provided in the gromacs pull code are position,
direction, and direction-periodic. For further details and more
thorough theoretical background visit gromacs manual at
http://manual.gromacs.org/documentation/2019-rc1/
reference- manual/special/pulling.html.
Acknowledgments
Special acknowledgment should be given to Assistant Prof. Justin
Lemkul for providing the comprehensive umbrella sampling tutorial available at www.mdtutorials.com/gmx/umbrella/index.html.
Special thanks to Mrs. Eleni Chontzopoulou for the extensive
tests to the comprehensibility of this protocol. This work was supported by the Hellenic Foundation for Research and Innovation
(HFRI) and the General Secretariat for Research and Technology
(GSRT), under the HFRI PhD Fellowship grant (GA. no. 14551).
The molecular dynamics simulations of this research work were
supported by computational time granted from the Greek Research
and Technology Network (GRNET) in the National HPC facility—ARIS—under project ID MDAT1R and from the ARIS
VI-SEEM HPC facility—under project ID AT1R. The research
leading to these results has been co-funded by the European
Commission under the H2020 Research Infrastructures contract
no. 675121 (project VI-SEEM).
Study of Candesartan Cilexetil: 2-Hydroxypropyl-β-Cyclodextrin Interactions…