[gmx-users] Can any body suggest me how do I generate the initial structure with the pre-quil. membrane and the small molecules put on top of it and check the effect of UV on it?

[Mark Abraham]

Subhrangshu Supakar wrote:
> Hi All,
> I want to check the interaction of my small molecule on the surface of a 
> lipid membrane for which I wish to use the pre-equillibrated structures 
> available with the gromacs web site.
> 1. Can any body suggest me how do I generate the initial structure with 
> the pre-quil. membrane and the small molecules put on top of it ?

With a molecule building program or with a text editor.

> 2. Is it possible to measure effect of UV radiation (any wavelength) on 
> the system where in the UV would be able to hit the lipid bilayer 
> passing through the small molecule layer?

No. What does UV normally do to chemical bonds? Are MD simulations 
useful in bond-breaking situations?

Mark