On 9/03/2012 7:19 AM, bo.shuang wrote:
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?
"Ions inside" is a bit vague for a description, but this kind of thing
is often a problem. Seee
http://www.gromacs.org/Documentation/How-tos/Parameterization
Mark
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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