[gmx-users] hydrophobic and hydrophilic in implicit solvent

[Justin A. Lemkul]

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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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