[gmx-users] OPLSaa+Lipid.itp question

[chris.neale at utoronto.ca]

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