VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Jul 20 2017 - 03:23:39 CDT

There is no single solution to this problem.
You can create your own (512 SDS molecule file) or find one already for
you.

To find one - maybe look at publications? or research groups that do
similar stuff. Some one might have something in their supplementary to
offer you.

To make your own - you can do one of two things (or more?):

e.g. I would either take a lipid monolayer/bilayer PDB with 512 lipid
molecules and replace each of them with the SDS you have.
or in a vacuum make copies of SDS randomly positioning them as long as
their is no structural overlap.

I don't see how you can avoid programming. Some solutions exist where you
can introduce your custom solvent instead of water when solvating a system.
You could look into that maybe and then delete the SDS molecules exceeding
your required count.

Maybe wait and someone else might offer a better solution.

Hope this helps.

Best,
/A

On Thu, Jul 20, 2017 at 6:42 PM, Siddharth Girdhar <
siddharth.gir47_at_gmail.com> wrote:

> Hi all,
>
> I am a beginner to VMD so this is probably a very silly question.
>
> What I currently have is a PDB and PSF file for the SDS molecule that I
> created and I want to solvate 512 of these molecules in a water box.
>
> How would I get along with doing that? I know how to get one SDS molecule
> solvated but how can I add 512 of them together?
>
> Thank you,
>
> Siddharth Girdhar
> 

-- 
Best,
/A