diff --git a/DATAreportediINblog/stereospecificOPs.pdf b/DATAreportediINblog/stereospecificOPs.pdf deleted file mode 100644 index cc7e949..0000000 Binary files a/DATAreportediINblog/stereospecificOPs.pdf and /dev/null differ diff --git a/Fig/Makefile b/Fig/Makefile index 4be0c62..07ec149 100644 --- a/Fig/Makefile +++ b/Fig/Makefile @@ -4,6 +4,7 @@ # For each figure, a serie of variables can be set (mainly for the location of the script # and for the path of the data files). The rule to generate the figure is below those. # The idea is to only re-generate the output when the dependencies (script or data) are changed. +# BE AWARE, all variables must have different names otherwise Makefile will fail. # # At the beginning of the Makefile, the output filename can be also changed. # @@ -13,7 +14,7 @@ ## Figure filenames ## ###################### dehydrationPN = dehydrationPN.pdf - +stereospecific = stereospecificOPs.pdf # Generate TARGETs from all filenames @@ -29,26 +30,51 @@ all: $(TARGETS) # Variables # ========= -SCRIPT = scripts/plotDehydrationPNvector.gpl -DATA_BERGER = ../DATAreportediINblog/POPC/dehydration/PN-vector/Berger-298K.dat -DATA_BERGER_DLPC = ../DATAreportediINblog/DLPC/dehydration/PN-vector/Berger-300K.dat -DATA_MACROG = ../DATAreportediINblog/POPC/dehydration/PN-vector/MacRog-310K.dat -DATA_CHARMM36 = ../DATAreportediINblog/POPC/dehydration/PN-vector/CHARMM36-303K.dat -DATA_GAFF = ../DATAreportediINblog/POPC/dehydration/PN-vector/GAFF-303K.dat +SCRIPT_DEHY = scripts/plotDehydrationPNvector.gpl +DEHY_BERGER = ../DATAreportediINblog/POPC/dehydration/PN-vector/Berger-298K.dat +DEHY_BERGER_DLPC = ../DATAreportediINblog/DLPC/dehydration/PN-vector/Berger-300K.dat +DEHY_MACROG = ../DATAreportediINblog/POPC/dehydration/PN-vector/MacRog-310K.dat +DEHY_CHARMM36 = ../DATAreportediINblog/POPC/dehydration/PN-vector/CHARMM36-303K.dat +DEHY_GAFF = ../DATAreportediINblog/POPC/dehydration/PN-vector/GAFF-303K.dat # Rule # ==== -$(dehydrationPN): $(SCRIPT) $(DATA_BERGER) $(DATA_MACROG) $(DATA_CHARMM36) $(DATA_GAFF) - gnuplot -e "OUTPUTFILE='$@'" -e "DATA_BERGER='$(DATA_BERGER)'" -e "DATA_BERGER_DLPC='$(DATA_BERGER_DLPC)'" \ - -e "DATA_MACROG='$(DATA_MACROG)'" -e "DATA_CHARMM36='$(DATA_CHARMM36)'" \ - -e "DATA_GAFF='$(DATA_GAFF)'" \ - $(SCRIPT) +$(dehydrationPN): $(SCRIPT_DEHY) $(DEHY_BERGER) $(DEHY_BERGER_DLPC) $(DEHY_MACROG) $(DEHY_CHARMM36) $(DEHY_GAFF) + gnuplot -e "OUTPUTFILE='$@'" -e "DATA_BERGER='$(DEHY_BERGER)'" -e "DATA_BERGER_DLPC='$(DEHY_BERGER_DLPC)'" \ + -e "DATA_MACROG='$(DEHY_MACROG)'" -e "DATA_CHARMM36='$(DEHY_CHARMM36)'" \ + -e "DATA_GAFF='$(DEHY_GAFF)'" \ + $(SCRIPT_DEHY) #------------# # end Figure # #------------# +#----------------------------------------------# +# Figure regarding the sterero specificity # +#----------------------------------------------# + +# Variables +# ========= +SCRIPT_STER = scripts/plotWithStereospecificity.gpl +STER_EXP = ../DATAreportediINblog/POPC-for-stereospecific/EXP-Ferreira2013.dat +STER_BERGER = ../DATAreportediINblog/POPC-for-stereospecific/BERGER-298K_recalculated-22-04-15.dat +STER_MACROG = ../DATAreportediINblog/POPC-for-stereospecific/MACROG-310K_recalculated-29-04-15.dat +STER_CHARMM36 = ../DATAreportediINblog/POPC-for-stereospecific/CHARMM36-303K_blogged-01-12-14.dat +STER_GAFF = ../DATAreportediINblog/POPC-for-stereospecific/GAFF-303K_blogged-12-11-14.dat + +# Rule +# ==== +$(stereospecific): $(SCRIPT_STER) $(STER_EXP) $(STER_BERGER) $(STER_MACROG) $(STER_CHARMM36) $(STER_GAFF) + gnuplot -e "OUTPUTFILE='$@'" -e "DATA_EXP='$(STER_EXP)'" -e "DATA_BERGER='$(STER_BERGER)'" \ + -e "DATA_MACROG='$(STER_MACROG)'" -e "DATA_CHARMM36='$(STER_CHARMM36)'" \ + -e "DATA_GAFF='$(STER_GAFF)'" \ + $(SCRIPT_STER) + +#------------# +# end Figure # +#------------# + clean: diff --git a/DATAreportediINblog/plotWithStereospecificity.gpl b/Fig/scripts/plotWithStereospecificity.gpl similarity index 71% rename from DATAreportediINblog/plotWithStereospecificity.gpl rename to Fig/scripts/plotWithStereospecificity.gpl index 198e207..74fbc5e 100644 --- a/DATAreportediINblog/plotWithStereospecificity.gpl +++ b/Fig/scripts/plotWithStereospecificity.gpl @@ -1,5 +1,5 @@ set term pdfcairo enhanced rounded color dashed dashlength 1 size 10cm, 21cm #16.2cm -set out "stereospecificOPs.pdf" +set out OUTPUTFILE # write name of the blog on the plot: # set label 1 right at screen 0.982,0.995 "nmrlipids.blogspot.fi" font ",9" tc rgb "gray" @@ -49,17 +49,12 @@ set linetype 24 lt 1 lw w lc rgb "#FFD300" # for GAFF set linetype 30 lt 1 lw w lc rgb "#00A368" # for MacRog plot [0.5:7.5][0.152659:-0.26] \ - "./POPC-for-stereospecific/BERGER-298K_recalculated-22-04-15.dat" u ($1-0.4):($2):($3) w ye lt 21 pt 7 ps r \ - t "{298K} Berger", \ - "./POPC-for-stereospecific/MACROG-310K_recalculated-29-04-15.dat" u ($1-0.2):($2):($3) w ye lt 30 pt 7 ps r \ - t "{310K} MacRog", \ - "./POPC-for-stereospecific/EXP-Ferreira2013.dat" u ($1):($2):($3) w ye lt 101 pt 7 ps 1.5*r \ - t "300K ^{_{^{13}}}C-NMR", \ + DATA_BERGER u ($1-0.4):($2):($3) w ye lt 21 pt 7 ps r t "{298K} Berger", \ + DATA_MACROG u ($1-0.2):($2):($3) w ye lt 30 pt 7 ps r t "{310K} MacRog", \ + DATA_EXP u ($1):($2):($3) w ye lt 101 pt 7 ps 1.5*r t "300K ^{_{^{13}}}C-NMR", \ x w p ls 1 ps 0 t " ", \ - "./POPC-for-stereospecific/GAFF-303K_blogged-12-11-14.dat" u ($1+0.2):($2):($3) w ye lt 24 pt 7 ps r \ - t "{303K} GAFFlipid", \ - "./POPC-for-stereospecific/CHARMM36-303K_blogged-01-12-14.dat" u ($1+0.4):($2):($3) w ye lt 23 pt 7 ps r \ - t "@{\\ \\ \"}&{303K} CHARMM36" + DATA_GAFF u ($1+0.2):($2):($3) w ye lt 24 pt 7 ps r t "{303K} GAFFlipid", \ + DATA_CHARMM36 u ($1+0.4):($2):($3) w ye lt 23 pt 7 ps r t "@{\\ \\ \"}&{303K} CHARMM36" diff --git a/Fig/stereospecificOPs.pdf b/Fig/stereospecificOPs.pdf new file mode 100644 index 0000000..e1744d2 Binary files /dev/null and b/Fig/stereospecificOPs.pdf differ diff --git a/HGmodelMANUSCRIPT/HGmodel_ACStemplate.pdf b/HGmodelMANUSCRIPT/HGmodel_ACStemplate.pdf index d475e8e..7f4c12f 100644 Binary files a/HGmodelMANUSCRIPT/HGmodel_ACStemplate.pdf and b/HGmodelMANUSCRIPT/HGmodel_ACStemplate.pdf differ diff --git a/HGmodelMANUSCRIPT/HGmodel_ACStemplate.tex b/HGmodelMANUSCRIPT/HGmodel_ACStemplate.tex index 8f87cd4..b134a7d 100644 --- a/HGmodelMANUSCRIPT/HGmodel_ACStemplate.tex +++ b/HGmodelMANUSCRIPT/HGmodel_ACStemplate.tex @@ -596,7 +596,7 @@ \subsection{Full hydration: Experimental order parameters for the glycerol backb and the stereospecific labeling from~\cite{gally81}, and shown in Fig.~\ref{HGorderparameters2}. \begin{figure*}[] \centering - \includegraphics[width=8.6cm]{../DATAreportediINblog/stereospecificOPs.pdf} \\ + \includegraphics[width=8.6cm]{../Fig/stereospecificOPs.pdf} \\ \caption{\label{HGorderparameters2} Order parameteres for POPC glycerol and choline groups from simulations with Berger-POPC-07, MacRog, GAFFlipid, and CHARMM36 force fields