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NMRLipids / lipid_ionINTERACTION

Files related to the NMRlipids II project
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POPC_LIPID14_CaCl_035M_1M #10

Closed MykhailoGirych closed 8 years ago

MykhailoGirych commented 8 years ago

0.35M and 1M CaCl2 (35 and 100 Ca) with 128 POPC and water/lipid 50/1 in LIPID14. 298C, CHARMM-GUI starting structure: -scripts for density and order parameter calculation -Ca density profiles (every 50ns) -box size vs time (both run and npt) -order parameters

I also added MAPPING folder to lipid_ionINTERACTION root with mapping files from NmrLipidsCholXray and new LIPID14 mapping file.

ohsOllila commented 8 years ago

Thanks! I looked at the density plots and with subjective estimation I would say that it would be better to use only the last 100ns of the trajectories. It seems that the Ca affinity is increasing during the first 100ns. Could you run the order parameter and density calculations only over the last 100ns?

Otherwise, I plotted the current order parameter results for 350mM system and the CaCl_2 effect seems to be significantly overestimated. This result will most likely not change but I think that it is better to use only the last 100ns anyway.