Hi,<br><br>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?<br>
<br>Thank you!<br><br>Bo<br><br>bo.shuang wrote:<br>
> For example, if I want to simulate how Membrane phospholipid bilayer<br>
> form its configuration in water, and want to use CG model and implicit<br>
> solvent, then I need the heads of these phospholipid molecules to be<br>
> hydrophilic and their tail to be hydrophobic. How can I specify<br>
> parameter of these particles to make them have these different<br>
> properties in implicit solvent?<br>
> It just an example. Hydrophobic also play important role in protein and<br>
> DNA folding. That's why I want to make hydrophobic work in implicit<br>
> solvent. Thank you very much for your help!<br>
><br>
<br>
Hydrophobicity and hydrophilicity are functions of the nonbonded parameters<br>
(charges and van der Waals parameters) of the individual atom types, which are<br>
essential components of a force field. There's nothing extra you need to do<br>
beyond defining these parameters (or using those that already exist).<br>
<br>
-Justin<br>