[gmx-users] Gromacs Simulation Question

Academic Research ac.research at icloud.com
Fri Jan 6 23:14:55 CET 2017

Hello everyone,

I have computationally designed several synthetic proteins that are not found in nature.

My lab has limited resources for wet lab work and so I would like to use gromacs to simulate these proteins in water and see weather they unfold or aggregate. I know the best way is to actually express and purify these proteins and observe them, but my idea is to use molecular simulation to screen through these designed proteins and priorities the ones that appear not to unfold nor aggregate.

1. From your experiences, does my idea sound so crazy that I should abandon it?

2. Does the Lysozyme in water tutorial from the Bevan Lab a good starting point?

3. Are there existing tutorials or papers that simulate protein unfolding or aggregation that I could use as a starting point?

Much appreciated,

AC Research

More information about the gromacs.org_gmx-users mailing list