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