read.plumed: Read 1D or 2D free energy surface from PLUMED sum_hills

In metadynminer: Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed'

Read 1D or 2D free energy surface from PLUMED sum_hills

Description

'read.plumed' reads 1D or 2D free energy surface from PLUMED sum_hills. The grid in the (2D) inputfile must contain the same number of points for CV1 and CV2. It does not use the header of the file. Instead, user must specify the dimensionality (1 or 2). Periodicity must be specified as well.

Usage

read.plumed(file = "fes.dat", dim = 2, per = c(F, F, F))

Arguments

file	input file from PLUMED sum_hills.
per	logical vector specifying periodicity of collective variables.
dim	dimension (1 or 2, default 2).

Value

fes object.

Examples

l1<-"-3.142 -124.8 -44.76"
l2<-"-3.117 -125.9 -43.05"
l3<-"-3.092 -126.9 -41.22"
l4<-"-3.068 -127.9 -39.36"
l5<-"-3.043 -128.8 -37.45"
fourpoints<-c(l1,l2,l3,l4)
tf <- tempfile()
writeLines(fourpoints, tf)
read.plumed(tf, dim=1, per=c(TRUE,TRUE))

metadynminer documentation built on April 14, 2022, 5:06 p.m.