[gmx-users] SDS micelle simulation in TFE solvent

[Peter C. Lai]

On 2012-12-19 10:16:09AM +0530, Archana Sonawani wrote:
> Hi,
> 
>   I want to simulate a peptide using SDS micelle. The peptide is random
> coil,
>     but I want it to be helical; therefore, I will use TFE for inducing
> helix.

You use TFE in a wet lab to physically induce helicity in real life. For
a simulation, there is no guarantee that the forcefield you are using will
behave in the same way. Might as well just use distance restraints to force
the helicity. 

>     I have never performed simulations using micelle. I have following
> queries:
>     1. *From where would I get coordinates of SDS micelle-water complex? *(
> I
>     have .itp file for SDS)

the g_membed introduciton page has an example of embedding in a POPE micelle.
http://wwwuser.gwdg.de/~ggroenh/membed.html

You can probably conduct a literature search and find a paper that provides
a pdb for an SDS micelle.


>     2. Do I require lipid.itp for this simulation?

you say you already have a .itp for SDS that works your chosen forcefield?