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
--
========================================
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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