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On 9/03/2012 7:19 AM, bo.shuang wrote:
<blockquote
cite="mid:CA+4uorP=Dxf4=RbB_bRZ8KQ-fc1b3Dn5ytkgpe3Mw0+wtawC_A@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
"Ions inside" is a bit vague for a description, but this kind of
thing is often a problem. Seee <a
href="http://www.gromacs.org/Documentation/How-tos/Parameterization">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CA+4uorP=Dxf4=RbB_bRZ8KQ-fc1b3Dn5ytkgpe3Mw0+wtawC_A@mail.gmail.com"
type="cite">
<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>
<br>
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