[gmx-users] Re: Re: hydrophobic and hydrophilic in implicit solvent

[bo.shuang]

Hi,

Thank you for your answer. May I ask where I can find the right parameter
in gbsa.itp for ions? These should be very basic things in simulation, but
I cannot find their parameters anywhere. How do you guys use implicit
solvent if you want to have ions inside?

Thank you!

Bo

bo.shuang wrote:
> For example, if I want to simulate how Membrane phospholipid bilayer
> form its configuration in water, and want to use CG model and implicit
> solvent, then I need the heads of these phospholipid molecules to be
> hydrophilic and their tail to be hydrophobic. How can I specify
> parameter of these particles to make them have these different
> properties in implicit solvent?
> It just an example. Hydrophobic also play important role in protein and
> DNA folding. That's why I want to make hydrophobic work in implicit
> solvent. Thank you very much for your help!
>

Hydrophobicity and hydrophilicity are functions of the nonbonded parameters
(charges and van der Waals parameters) of the individual atom types, which
are
essential components of a force field.  There's nothing extra you need to do
beyond defining these parameters (or using those that already exist).

-Justin
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