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

bo.shuang bs16 at rice.edu
Thu Mar 8 21:19:40 CET 2012


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.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
essential components of a force field.  There's nothing extra you need to do
beyond defining these parameters (or using those that already exist).

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