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
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