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electrolytes

README.md

Electrolytes

TBA & TEA

Merged topology from LigParGen with nonbonded parameters from 2014JNCanongiaLopes-JPCB. Charged are subsequently scaled by 0.8 following 2017BDoherty-JCTC.

PF6, BF4, ClO4, & OTf

From https://github.com/orlandoacevedo/IL:

mkdir -p PF6_08scaled
cp IL/0.8\*2009IL/ITP/PF6_scale0.8.itp           PF6_08scaled/PF6_08scaled.itp
cp IL/0.8\*2009IL/ITP/PF6_atomtypes_scale0.8.itp PF6_08scaled/PF6_atomtypes_08scaled.itp
cp IL/PDB/PF6.pdb                                PF6_08scaled/.

mkdir -p BF4_08scaled
cp IL/0.8\*2009IL/ITP/BF4_scale0.8.itp           BF4_08scaled/BF4_08scaled.itp
cp IL/0.8\*2009IL/ITP/BF4_atomtypes_scale0.8.itp BF4_08scaled/BF4_atomtypes_08scaled.itp
cp IL/PDB/BF4.pdb                                BF4_08scaled/.

mkdir -p ClO4_08scaled
cp IL/0.8\*2009IL/ITP/ClO4_scale0.8.itp           ClO4_08scaled/ClO4_08scaled.itp
cp IL/0.8\*2009IL/ITP/ClO4_atomtypes_scale0.8.itp ClO4_08scaled/ClO4_atomtypes_08scaled.itp
cp IL/PDB/ClO4.pdb                                ClO4_08scaled/.

mkdir -p OTf_08scaled
cp IL/0.8*2009IL/ITP/TFO_scale0.8.itp           OTf_08scaled/OTf_08scaled.itp
cp IL/0.8*2009IL/ITP/TFO_atomtypes_scale0.8.itp OTf_08scaled/OTf_atomtypes_08scaled.itp
cp IL/PDB/TFO.pdb                               OTf_08scaled/OTf.pdb
# Just rename the anion from TFO to OTf (by replacing TFO occurrences inside the files)
cd OTf_08scaled
sed -i '' 's/TFO/OTf/' *
cd ..

Li

echo "[ atomtypes ]"                                              >  Li_08scaled/Li_atomtypes_08scaled.itp
echo "; scaled by 0.8"                                            >> Li_08scaled/Li_atomtypes_08scaled.itp
echo "; name  mass  charge  ptype   sigma   epsilon"              >> Li_08scaled/Li_atomtypes_08scaled.itp
grep opls_406 /usr/local/gromacs/share/gromacs/top/oplsaa.ff/*itp >> Li_08scaled/Li_atomtypes_08scaled.itp