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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