Thanks Oliver, it's gratifying to know that everything is working for
you. If you are not using the half-epsilon double-pairlist method for
the lipid 1-4 interactions then you should note that opls-aa defaults
are causing coulombic 1-4 scaling by 0.5 (non-standard for these lipid
parameters). Be aware that even with 100ns your calculated lateral
diffusion is sure to be much higher than experimental results because
you are still in the non-linear region of the MSD plot.
Good luck.
Hi Chris,
thank you very much for your help. My test simulation is coming along
well. The area per lipid is in good agreement with experimental values.
Also the embedded membrane protein behaves quite well in terms of
RMSD/F, but I have to play around with the protein insertion protocol.
Now I am just waiting for the simulation to pass the 100ns mark in order
to calculate reliable lateral diffusion data for the lipids.
Thanks a lot again!
regards
Oliver
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