read.plumed3d: Read 3D free energy surface from PLUMED sum_hills

In metadynminer3d: Tools to Read, Analyze and Visualize Metadynamics 3D HILLS Files from 'Plumed'

Read 3D free energy surface from PLUMED sum_hills

Description

'read.plumed3d' reads 3D free energy surface from PLUMED sum_hills. The grid in the inputfile must contain the same number of points for CV1, CV2 and CV3. It does not use the header of the file. Periodicity must be specified.

Usage

read.plumed3d(file = "fes.dat", per = c(FALSE, FALSE, FALSE))

Arguments

file	input file from PLUMED sum_hills.
per	logical vector specifying periodicity of collective variables.

Value

fes3d object.

Examples

l1<-" -3.14 -3.14 -3.14 -61.13 -47.43  19.00   2.04"
l2<-" -1.05 -3.14 -3.14 -70.72  25.95  25.78   2.43"
l3<-"  1.05 -3.14 -3.14 -65.58   8.34   2.82  -3.09"
l4<-" -3.14 -1.05 -3.14 -51.31 -43.88 -19.91   1.51"
l5<-" -1.05 -1.05 -3.14 -66.43   7.67 -22.45  -0.39"
l6<-"  1.05 -1.05 -3.14 -61.08  -7.50  -7.36  -0.83"
l7<-" -3.14  1.05 -3.14 -53.07 -55.12   0.19  -0.28"
l8<-" -1.05  1.05 -3.14 -62.81  36.19   1.65   0.45"
l9<-"  1.05  1.05 -3.14 -65.28  22.84  11.47   0.59"
l10<-" -3.14 -3.14 -1.05 -13.03 -32.17   8.24 -35.25"
l11<-" -1.05 -3.14 -1.05 -21.88  17.89  21.91 -51.20"
l12<-"  1.05 -3.14 -1.05 -14.49   3.60   6.04 -44.05"
l13<-" -3.14 -1.05 -1.05  -2.26  -7.00  -7.01 -10.65"
l14<-" -1.05 -1.05 -1.05  -8.21   3.69 -22.89 -28.48"
l15<-"  1.05 -1.05 -1.05  -1.10   0.52   3.59  -1.99"
l16<-" -3.14  1.05 -1.05  -3.75 -11.70  -5.65 -15.36"
l17<-" -1.05  1.05 -1.05  -1.15   5.75   1.05  -2.42"
l18<-"  1.05  1.05 -1.05 -10.67   8.23 -10.42 -36.77"
l19<-" -3.14 -3.14  1.05  -4.64 -13.79  10.51  14.96"
l20<-" -1.05 -3.14  1.05  -7.80  12.24  20.59  23.03"
l21<-"  1.05 -3.14  1.05  -5.32   3.46   3.17  21.99"
l22<-" -3.14 -1.05  1.05  -2.06  -6.59   0.17  10.04"
l23<-" -1.05 -1.05  1.05  -9.69   8.43  -0.97  36.97"
l24<-"  1.05 -1.05  1.05  -0.19  -0.44  -0.26   0.91"
l25<-" -3.14  1.05  1.05  -7.98 -23.02   3.97  26.98"
l26<-" -1.05  1.05  1.05  -4.64  13.66  -9.74  10.15"
l27<-"  1.05  1.05  1.05 -13.42  15.78  16.36  41.60"
twentysevenpoints<-c(l1,l2,l3,l4,l5,l6,l7,l8,l9,l10,
                     l11,l12,l13,l14,l15,l16,l17,l18,l19,l20,
                     l21,l22,l23,l24,l25,l26,l27)
tf <- tempfile()
writeLines(twentysevenpoints, tf)
read.plumed3d(tf, per=c(TRUE,TRUE,TRUE))

metadynminer3d documentation built on April 14, 2022, 5:08 p.m.