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NMRLipids / lipid_ionINTERACTION

Files related to the NMRlipids II project
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Lipid 14 simulations with CaCl_2 #60

Open ohsOllila opened 7 years ago

ohsOllila commented 7 years ago

These ones seems to have incorrect CaCl_2 concentrations in Table 1, figures and in Zenodo: M. Girych and O. H. S. Ollila, POPC_AMBERLIPID14 CaCl2_035Mol, 2015, DOI: 10.5281/zenodo.34415. M. Girych and O. H. S. Ollila, POPC_AMBER_LIPID14_CaCl2_1Mol, 2015, DOI: 10.5281/zenodo.35074.

Correct concentrations should be 304mM and 867mM.

Conclusions should not be affect by this.

markussmiettinen commented 7 years ago

Prompted by this, I checked the whole Table 1. The following systems seem to have incorrect salt concentrations:

Force field for lipids/ions Lipid Salt [Salt] in Table 1 correct [Salt]
Berger-DPPC-97/ffgmx DPPC NaCl 1000 1020
Berger-OPLS-DPPC-06/OPLS DPPC NaCl 1000 1020
CHARMM36/CHARMM36 POPC CaCl2 350 300
670 580
1000 870
Lipid14/AMBER POPC NaCl 150 130
1000 830
CaCl2 350 300
1000 870
Ulmschneiders/OPLS POPC NaCl 150 130
1000 830
markussmiettinen commented 7 years ago

To redo Fig. 2, here are the correct salt concentrations for Table 1, calculated from [salt] = #ions * 55500 mM / #waters.

Berger 0 339.072 341.204 0 154.167 1018.9

Berger-OPLS 0 154.167 1018.9

CHARMM36 0 0 346.043 692.086 947.186 303.516 450.167 581.016 867.188 0 429.124 885.638

MacRog 0 0 102.961 206.69 311.193 416.481

Orange 0 135.555 514.989 998.201 514.989

Slipids 0 129.5 450.167 0 151.083 849.034 1751.66 2574.42

Lipid14 0 130.078 834.668 303.516 867.188

Ulmschneiders 0 130.078 834.668

I don't think the conclusions change, but should we write an erratum?