[gmx-users] Lipids forming unsual bonds
Mark.Abraham at anu.edu.au
Thu May 21 06:40:07 CEST 2009
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
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