diff --git a/user-doc/tutorials/others/ves-lugano2017-01-metad.txt b/user-doc/tutorials/others/ves-lugano2017-01-metad.txt index f456a5956fb1f4ecbdabbc61847a6d35e4f90b52..0b1ef049843905f95c31c6dac3677a06dadfaaa8 100644 --- a/user-doc/tutorials/others/ves-lugano2017-01-metad.txt +++ b/user-doc/tutorials/others/ves-lugano2017-01-metad.txt @@ -29,7 +29,7 @@ We consider the association/dissociation of NaCl in acqueous solution. The dissociation barrier is expected to be around 2.5 \f$k_\mathrm{B} T\f$. One interesting aspect of the ion dissociation problem is that collective solvent motions play an important role in the transition. -This problem has been considered in the original metadynamics paper \cite metad +This problem has been considered in the original metadynamics paper \cite metad and also in reference \cite tps2 . We will use the potential developed in ref.\ \cite Pettitt-JCP-1986 for NaCl and TIP3P water with parameters corrected to be used with long-range Coulomb solvers \cite Price-JCP-2004. @@ -239,7 +239,7 @@ The scripts for this example can be found in the folder Bias_calculation. In this case we observe only the first 200 ps of the simulation. The (negative) bias can be calculated using: \verbatim -plumed sum_hills --hills ../HILLS --min 0.1 --max 0.8 --bin 300 --stride 100 --negbias +plumed sum_hills --hills ../HILLS --min 0.1 --max 0.8 --bin 300 --stride 10 --negbias \endverbatim This plot illustrates clearly how the bias is constructed to progressively "fill" the FES. \anchor ves-school-2017-metad-biasEvolution @@ -390,6 +390,7 @@ You will find a gnuplot script plot.gpi to make this plot inside the ReweightDis We can obtain important information of the system by reweighting on 2 CVs: The distance Na-Cl and the coordination of Na with O. This reweighting is similar to the one already done and the files that you will need are located in the ReweightBoth folder. +Additionally the COLVAR file with the omitted first steps is required. The plot of the FES as a function of these 2 CVs provides important information of the association/dissociation mechanism. In the dissociated state, Na can have a coordination of 5 or 6, though it is more @@ -454,7 +455,7 @@ and plot the results using the following lines in gnuplot: \verbatim set pm3d map set zr [0:15] -pl "fes.dat" u 1:2:3 +spl "fes.dat" u 1:2:3 \endverbatim \section ves-lugano2017-metad-final Final remarks diff --git a/user-doc/tutorials/others/ves-lugano2017-02-ves1.txt b/user-doc/tutorials/others/ves-lugano2017-02-ves1.txt index 8d2092babcba16d0a7a766c0c5be74f48c4feb26..0d88e7bdebf9b147331f0dbcd46b6a06ec80090f 100644 --- a/user-doc/tutorials/others/ves-lugano2017-02-ves1.txt +++ b/user-doc/tutorials/others/ves-lugano2017-02-ves1.txt @@ -447,7 +447,7 @@ continuously. As an exercise, you can use a target distribution consisting in a gaussian centered at the dissociation barrier. The syntax in Plumed is: \plumedfile -td1: TD_GAUSSIAN CENTER=0.325 SIGMA=0.03 +td1: TD_GAUSSIAN CENTER1=0.325 SIGMA1=0.03 VES_LINEAR_EXPANSION ... ARG=d1 diff --git a/user-doc/tutorials/others/ves-lugano2017-04-kinetics.txt b/user-doc/tutorials/others/ves-lugano2017-04-kinetics.txt index 6dde32977576c1f322edfdcd11493673175a5e16..be2e51cda510f184815393d00a5818e9d4038d85 100644 --- a/user-doc/tutorials/others/ves-lugano2017-04-kinetics.txt +++ b/user-doc/tutorials/others/ves-lugano2017-04-kinetics.txt @@ -178,7 +178,7 @@ We will also perform metadynamics with an infrequent deposition stride to ensure METAD ... ARG=CV1,CV2 SIGMA=0.2,0.2 - HEIGHT=0.15,0.15 + HEIGHT=0.15 PACE=4000 LABEL=metad ... METAD diff --git a/user-doc/tutorials/others/ves-lugano2017-metad/Example2/ReweightDistance/plot.gpi b/user-doc/tutorials/others/ves-lugano2017-metad/Example2/ReweightDistance/plot.gpi index acf15e2dc107ddc97bd21e74c31953415af7678a..29284bde0028dae1d561b21dae81a9dca740b850 100644 --- a/user-doc/tutorials/others/ves-lugano2017-metad/Example2/ReweightDistance/plot.gpi +++ b/user-doc/tutorials/others/ves-lugano2017-metad/Example2/ReweightDistance/plot.gpi @@ -19,7 +19,7 @@ set key bottom left sample 1. everyValue=1 -pl "../fes-mintozero/fes_77.dat" u 1:($2/2.494) w l ls 1 title "sum hills", \ +pl "../Bias_calculation/fes.dat" u 1:($2/2.494) w l ls 1 title "sum hills", \ "./histo" u 1:(-log($2)+2.15) every everyValue w p ls 2 title "Reweight", \ "./histo_wall" u 1:(-log($2)+1.3) every everyValue w p ls 3 title "Reweight w/ wall bias" diff --git a/user-doc/tutorials/others/ves-lugano2017-ves1/Example1/Barrier_calculation/run.sh b/user-doc/tutorials/others/ves-lugano2017-ves1/Example1/Barrier_calculation/run.sh deleted file mode 100755 index ccf5290896e786378b84e901e20778337ff41a2c..0000000000000000000000000000000000000000 --- a/user-doc/tutorials/others/ves-lugano2017-ves1/Example1/Barrier_calculation/run.sh +++ /dev/null @@ -1 +0,0 @@ -plumed sum_hills --hills ../HILLS --min 0.1 --max 0.8 --bin 300 --stride 100 --mintozero diff --git a/user-doc/tutorials/others/ves-lugano2017-ves1/Example2/plotTargetDistrib.gpi b/user-doc/tutorials/others/ves-lugano2017-ves1/Example2/plotTargetDistrib.gpi index f853cd87b13614212c889223071315941e99cee2..8db446debe1fbb17aa07890ded56789e4841d17f 100644 --- a/user-doc/tutorials/others/ves-lugano2017-ves1/Example2/plotTargetDistrib.gpi +++ b/user-doc/tutorials/others/ves-lugano2017-ves1/Example2/plotTargetDistrib.gpi @@ -1,7 +1,7 @@ # Terminal settings -set terminal pngcairo size 1000,600 enhanced font 'Verdana,18' -set output "plotTD.png" -set border lw 1.5 +#set terminal pngcairo size 1000,600 enhanced font 'Verdana,18' +#set output "plotTD.png" +#set border lw 1.5 # Set labels set xlabel "Distance (nm)"