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Use of solvent ions in martini
- rcorey
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8 years 11 months ago #4563
by rcorey
Use of solvent ions in martini was created by rcorey
Hello
I notice on several martini tutorials (using Gromacs) the system is solvated with water molecules but not counter ions (e.g. Na+Cl-).
Is there a reason for this, i.e. does the inclusion of ions not make sense with regard to the fundamental principles of coarse grain (salt-bridges etc.)? I'm new to the field and am keen to understand some of the basic elements of coarse grain in a bit more detail.
Many thanks
Robin
I notice on several martini tutorials (using Gromacs) the system is solvated with water molecules but not counter ions (e.g. Na+Cl-).
Is there a reason for this, i.e. does the inclusion of ions not make sense with regard to the fundamental principles of coarse grain (salt-bridges etc.)? I'm new to the field and am keen to understand some of the basic elements of coarse grain in a bit more detail.
Many thanks
Robin
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- helgi
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8 years 4 months ago #5283
by helgi
Replied by helgi on topic Use of solvent ions in martini
Sorry for the very slow answer.
In regular Martini simulations it’s not nearly as important to add ions as in atomistic simulations e.g. all the electrostatics are scaled down: dielectric screening of 15, no partial charges, etc. Martini ions for example are considered to be partially hydrated (each ion bead is the ion + a few waters).
But this of course will depend on the system in question and for some Martini systems electrostatics can play a larger role, especially if you use polarizable water (a lower dielectric screening) or PME.
Cheers,
- Helgi
In regular Martini simulations it’s not nearly as important to add ions as in atomistic simulations e.g. all the electrostatics are scaled down: dielectric screening of 15, no partial charges, etc. Martini ions for example are considered to be partially hydrated (each ion bead is the ion + a few waters).
But this of course will depend on the system in question and for some Martini systems electrostatics can play a larger role, especially if you use polarizable water (a lower dielectric screening) or PME.
Cheers,
- Helgi
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- rcorey
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8 years 4 months ago - 8 years 4 months ago #5284
by rcorey
Replied by rcorey on topic Use of solvent ions in martini
Ah - ok. That's really interesting, thanks for the reply! better late than never :-)
Many thanks
Robin
Many thanks
Robin
Last edit: 8 years 4 months ago by rcorey.
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