README.md

In sucurz/testing: Metadynminer reads, analyses and visualizes metadynamics HILLS files from Plumed.

Metadynminer

Metadynminer is R packages for reading, analysis and visualisation of metadynamics HILLS and COLVAR files produced by Plumed.

```R

Install from R repository

install.packages("metadynminer") # in future will be added to R repository

Load library

library(metadynminer) # in future will be added to R repository

Read hills file

hills<-read.hills("HILLS", per=c(TRUE, TRUE)) # done

Sum two hills files

hills+hills # done

Summary of a hills file

summary(hills) # done

Plot CVs

plot(hills) # done

Plot heights

plotheights(hills) # done

Calculate FES by bias sum (alternatively use fes2 for conventional calculation)

fes<-fes(hills, tmin=5000, tmax=10000) # done, to do manual

Sum two FESes

fes+fes # done, to do manual

Calculate and substract min, max or mean from a FES

fes<-fes+min(fes1) # done, to do manual

Summary of FES

summary(fes) # done, to do manual

Plot FES

plot(fes) # done

In order to make a movie you can use summation of FESes

tfes<-fes(hills, tmax=1000) png("test%03d.png") plot(tfes, zlim=c(-120,0)) for(i in 1:10) { tfes<-tfes+fes(hills, tmin=1000i+1, tmax=1000(i+1)) plot(tfes, zlim=c(-120,0)) } dev.off()

Find minima

minima<-fesminima(fes) # done, to do manual

Summary of minima

summary(minima) # done, to do manual

Create empty minima

minima<-emptyminima(fes) # done, to do manual

Create ad hoc minimum

minima<-oneminimum(fes, cv1=0, cv2=0) # done, to do manual

sum minima

fesminima(fes) + oneminimum(fes, cv1=0, cv2=0) # done, to do manual

Plot free energy minima

plot(minima) # 2D done, 1D to do, to do manual

Calculate free energy profile for minima

prof<-feprofiles(hills, minima) # done, to do manual

Find transition path

Summary of transition path

Minima areas

Reweight

sucurz/testing documentation built on May 29, 2019, 9:51 a.m.