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Lipid 14 simulations with CaCl_2 #60

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ohsOllila opened this issue Mar 17, 2017 · 2 comments
Open

Lipid 14 simulations with CaCl_2 #60

ohsOllila opened this issue Mar 17, 2017 · 2 comments

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@ohsOllila
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These ones seems to have incorrect CaCl_2 concentrations in Table 1, figures and in Zenodo:
M. Girych and O. H. S. Ollila, POPC_AMBER_LIPID14_ 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
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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
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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?

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