Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
Photo
- - - - -

Pigment containing protein complex molecular dynamics using NAMD

Molecular Dynamics NAMD protein analysis

  • Please log in to reply
No replies to this topic

#1 Belzebud

Belzebud

    member

  • Active Members
  • Pip
  • 7 posts
0
Neutral

Posted 24 October 2012 - 05:41 AM

Hi,

Part of my PhD involves doing some molecular dynamics between protein pigment containing complexes. I aiming to see how certain pigments within each complex influence the aggregation process under certain conditions.

I have no experience in molecular dynamics, but I'm working through the VMD/NAMD tutorials.

However, I'm not sure, if the I should include the pigments with the proteins when generating segment individual the psf files.

I do know that:
- only 2 of the large number of pigments should be involved in the process I want to analyze
- all of the pigments, except from one of the 2, have structural importance for the folding of the protein

The dynamics will be checked within a lipid membrane.

I hope I've explained the problem in and understandable way.

So, my questions are:

- should I include the pigments with the protein strands in the segments during psf generation
- any advice on finding the best sequence of doing tutorials related to molecular dynamics using NAMD

Thanks

Edited by Belzebud, 24 October 2012 - 05:45 AM.





Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.