[gmx-users] Lipids forming unsual bonds

[Mark Abraham]

Anirban Ghosh wrote:
> Hi ALL,
> 
> I am simulating a GPCR protein in a POPC bilayer.
> I have followed Justins' tutorial to set up the system, but have used 
> POPC instead of DPPC. I have used the same parameters given in that 
> tutorial. Till equilibration everything went well. But after releasing 
> the protein in the production MD, the lipids are forming usual cross 
> bonds (seen in the form of long straight lines). How can I avoid this? 
> Any suggestion is welcome.

Bonds don't form in MD. Probably, the heuristic that your visualization 
software is using to guess where bonds exist isn't working the way you 
expected. I can't tell from your description, but you may being seeing 
"bonds" across the simulation box when the periodic boundaries intersect 
with molecules.

Mark