Hello:

I am simulating a stearol sphingomyelin bilayer with 81 lipids in each leaflet 
using the CHARMM force field. I used the CHARMM-GUI to generate the initial 
conformation, as well as the parameters for mdp file. I conducted the 
simulation by gmx5.0.4. 


I found a significant smaller area per lipid (APL) in my simulations. The APL 
kept on decreasing, and started to equilibriated after 400 ns. The expected 
value is ~55.4 A^2, but in my simulation, the value was ~50.8 A^2 after 
equilibrated. For me this difference is significant. I looked up in the mailing 
list, and found someone said that it is because of the ions using or it is 
because of the motion of the two leaflets. So I tried simulations without ions, 
and with NaCl/KCl. I also tried to remove the centers of mass of two leaflets 
separately in my simulations. But all of the simulations generated similar APL. 


I am really appreciate for any possible suggestions. This looks really strange 
for me, as I am using the "standard parameters" (i.e., the parameters generated 
by CHARMM-GUI) for CHARMM force filed in gromacs, and the difference should not 
be so larger, if there are any differences....


Thanks again for any help you may provide. 


Cheers, 
RXG
University of Calgary
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