Package 'metadynminer3d'

Title: Tools to Read, Analyze and Visualize Metadynamics 3D HILLS Files from 'Plumed'
Description: Metadynamics is a state of the art biomolecular simulation technique. 'Plumed' Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> program makes it possible to perform metadynamics using various simulation codes. The results of metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package 'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package. As an addendum, 'metadynaminer3d' is used to visualize 3D hills. It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037> to calculate a free energy surface from hills. Minima can be located and plotted on the free energy surface. Free energy surfaces and minima can be plotted to produce publication quality images.
Authors: Vojtech Spiwok [aut, cre]
Maintainer: Vojtech Spiwok <[email protected]>
License: GPL-3
Version: 0.0.2
Built: 2025-01-31 04:39:30 UTC
Source: https://github.com/cran/metadynminer3d

Help Index

Hills from 30 ns metadynamics of AceAlaNme in water with three collective variable

Description

Hills from 30 ns metadynamics of AceAlaNme (Amber99SB-ILDN) in water (TIP3P) with a Ramachandran dihedral phi and psi and peptide bond torsion omega as the collective variable.

Usage

acealanme3d

Format

hillsfile3d object

Source

http://www.metadynamics.cz/metadynminer/data/HILLS3d

Calculate free energy profile for minima3d object

Description

'feprof.minima3d' calculates free energy profiles for free energy minima. It finds the global minimum at the 'imax' and calculates the evolution of free energies of a local vs. the global free energy minimum. The free energy of the global minimum is constant (zero).

Usage

## S3 method for class 'minima3d'
feprof(minims, imax = NULL)

Arguments

minims

minima3d object.
imax

index of a hill from which summation stops (default the rest of hills).

Examples

library(metadynminer3d)
tfes<-fes(acealanme3d, imax=5000)
minima<-fesminima(tfes)
prof<-feprof(minima)
prof

Calculate 3D free energy surface by Bias Sum algorithm

Description

'fes.hillsfile3d' sums up hills using fast Bias Sum algorithm.

Usage

## S3 method for class 'hillsfile3d'
fes(hills, imin = 1, imax = NULL, xlim = NULL,
  ylim = NULL, zlim = NULL, npoints = NULL)

Arguments

hills

hillsfile3d object.
imin

index of a hill from which summation starts (default 1).
imax

index of a hill from which summation stops (default the rest of hills).
xlim

numeric vector of length 1, giving the CV2 coordinates range.
ylim

numeric vector of length 2, giving the CV2 coordinates range.
zlim

numeric vector of length 2, giving the CV3 coordinates range.
npoints

resolution of the free energy surface in number of points.

Value

fes object.

Examples

tfes<-fes(acealanme3d, imax=5000)

Calculate 3D free energy surface by conventional algorithm

Description

'fes2.hills3d' sums up hills using slow conventional algorithm. It can be used as a reference or when hill widths are variable.

Usage

## S3 method for class 'hillsfile3d'
fes2(hills, imin = 1, imax = NULL, xlim = NULL,
  ylim = NULL, zlim = NULL, npoints = NULL)

Arguments

hills

hillsfile3d object.
imin

index of a hill from which summation starts (default 1).
imax

index of a hill from which summation stops (default the rest of hills).
xlim

numeric vector of length 2, giving the CV1 coordinates range.
ylim

numeric vector of length 2, giving the CV2 coordinates range.
zlim

numeric vector of length 2, giving the CV3 coordinates range.
npoints

resolution of the free energy surface in number of points.

Value

fes object.

Examples

tfes<-fes2(acealanme3d, imax=100)

Find free energy minima in the fes3d object

Description

'fesminima.fes3d' finds free energy minima on 3D free energy surface. The surface is divided by a 3D grid and minima are found for each bin. Next the program determines whether the minimum of a bin is a local minimum of the whole free energy surface. Free energy minima are labeled constitutively by capital letters.

Usage

## S3 method for class 'fes3d'
fesminima(inputfes, nbins = 8)

Arguments

inputfes

fes3d object.
nbins

number of bins for each CV (default 8).

Value

minima object.

Examples

tfes<-fes(acealanme3d, imax=5000)
minima<-fesminima(tfes)
minima

Calculate free energy at given point in the CV space

Description

‘fespoint' calculates free energy at given point in the CV space ’coord'. Hills are summed from 'imin' to 'imax'. Printed output can be suppressed by setting 'verb' to TRUE.

Usage

## S3 method for class 'hillsfile3d'
fespoint(hills, coord = NULL, imin = 1,
  imax = NULL, verb = T)

Arguments

hills

hillsfile3d object.
coord

coordinates of the point in the CV space.
imin

index of a hill from which calculation of difference starts (default 1).
imax

index of a hill from which summation stops (default the rest of hills).
verb

if TRUE, the output is verbose (default TRUE).

Examples

fespoint(acealanme3d, c(0,0,0), imax=5000)

Print first n lines of hillsfile3d

Description

'head.hillsfile3d' prints first n lines of a hillsfile3d object.

Usage

## S3 method for class 'hillsfile3d'
head(x, n = 10, ...)

Arguments

x

hillsfile3d object.
n

number of lines (default 10).
...

further arguments passed to or from other methods.

Examples

head(acealanme3d)

Calculate maximum of 3D free energy surface

Description

'max.fes3d' calculates maximum of free energy in a fes3d object.

Usage

## S3 method for class 'fes3d'
max(inputfes, na.rm = NULL, ...)

Arguments

inputfes

fes3d object.
na.rm

a logical indicating whether missing values should be removed.
...

further arguments passed to or from other methods.

Examples

tfes<-fes(acealanme3d, imax=5000)
max(tfes)

Calculate minimum of 3D free energy surface

Description

'min.fes3d' calculates minimum of free energy in a fes3d object.

Usage

## S3 method for class 'fes3d'
min(inputfes, na.rm = NULL, ...)

Arguments

inputfes

fes3d object.
na.rm

a logical indicating whether missing values should be removed.
...

further arguments passed to or from other methods.

Examples

tfes<-fes(acealanme3d, imax=5000)
min(tfes)

Creates one ad hoc 3D free energy minimum for a fes object

Description

'oneminimum.fes3d' creates an ad hoc 3D free energy minimum on free energy surface. This can be used to calculate 3D free energy surface evolution at arbitrary point of free energy surface.

Usage

## S3 method for class 'fes3d'
oneminimum(inputfes, cv1, cv2, cv3)

Arguments

inputfes

fes3d object.
cv1

the value of collective variable 1.
cv2

the value of collective variable 2.
cv3

the value of collective variable 3.

Value

minima object.

Examples

tfes<-fes(acealanme3d, imax=1000)
minima<-fesminima(tfes)
minima<-minima+oneminimum(tfes, cv1=0, cv2=0, cv3=0)
minima

Plot 3D free energy surface object

Description

'plot.fes3d' plots 3D free energy surface using .

Usage

## S3 method for class 'fes3d'
plot(x, xlab = NULL, ylab = NULL, zlab = NULL, 
  xlim = NULL, ylim = NULL, zlim = NULL, level = NULL,
  col = NULL, alpha = NULL, main = NULL, sub = NULL, fill = TRUE, ...)

Arguments

x

fes3d object.
xlab

a title for the x axis: see 'title'.
ylab

a title for the y axis: see 'title'.
zlab

a title for the z axis: see 'title'.
xlim

numeric vector of length 2, giving the x coordinates range.
ylim

numeric vector of length 2, giving the y coordinates range.
zlim

numeric vector of length 2, giving the z coordinates range.
main

an overall title for the plot: see 'title'.
sub

a sub title for the plot: see 'title'.
level

number or numeric vector of levels at which to draw 3D isosurface.
col

color of the free energy surface. It can be a single color or a vector with multiple colors for multiple 3D isosurfaces.
alpha

number or numeric vector of alpha levels (transparency) of 3D isosurfaces.
fill

a logical value indicating whether 3D isosurface is ploted as solid surface (True) or wireframe (False).
...

further arguments passed to or from other methods.

Examples

tfes3d<-fes(acealanme3d, imax=5000)
plot(tfes3d)

Plot hillsfile3d object

Description

'plot.hillsfile3d' plots hillsfile object. It plots CV1 vs CV2 vs CV3.

Usage

## S3 method for class 'hillsfile3d'
plot(x, xlab = "CV1", ylab = "CV2", zlab = "CV3",
  main = NULL, sub = NULL, col = "orange", ...)

Arguments

x

hillsfile object.
xlab

a title for the x axis: see 'title'.
ylab

a title for the y axis: see 'title'.
zlab

a title for the z axis: see 'title'.
main

an overall title for the plot: see 'title'.
sub

a sub title for the plot: see 'title'.
col

color code or name, see 'par'.
...

further arguments passed to or from other methods.

Examples

plot(acealanme3d)

Plot minima3d object

Description

'plot.minima3d' plots 3D free energy surface with minima. The free energy surface is plotted the same way as by plot.fes3d with additional minima labels.

Usage

## S3 method for class 'minima3d'
plot(x, xlab = "CV1", ylab = "CV2", zlab = "CV3", level = NULL,
  col = NULL, alpha = NULL, main = NULL, sub = NULL, fill = TRUE, ...)

Arguments

x

minima3d object.
main

an overall title for the plot: see 'title'.
sub

a sub title for the plot: see 'title'.
xlab

a title for the x axis: see 'title'.
ylab

a title for the y axis: see 'title'.
zlab

a title for the z axis: see 'title'.
level

number or numeric vector of levels at which to draw 3D isosurface.
col

color of the free energy surface. It can be a single color or a vector with multiple colors for multiple 3D isosurfaces.
alpha

number or numeric vector of alpha levels (transparency) of 3D isosurfaces.
fill

a logical value indicating whether 3D isosurface is ploted as solid surface (True) or wireframe (False).
...

further arguments passed to or from other methods.

Examples

tfes<-fes(acealanme3d, imax=5000)
minima<-fesminima(tfes)
plot(minima)

Plot evolution of heights of hills in hillsfile3d object

Description

'plotheights.hillsfile3d' plots evolution of heights of hills. In well tempered metadynamics hill heights decrees with flooding of the free energy surface. Evolution of heights may be useful to evaluate convergence of the simulation.

Usage

## S3 method for class 'hillsfile3d'
plotheights(hills, ignoretime = FALSE, xlab = NULL,
  ylab = NULL, xlim = NULL, ylim = NULL, main = NULL, sub = NULL,
  col = "black", asp = NULL, lwd = 1, axes = TRUE)

Arguments

hills

hillsfile object.
ignoretime

time in the first column of the HILLS file will be ignored.
xlab

a title for the x axis: see 'title'.
ylab

a title for the y axis: see 'title'.
xlim

numeric vector of length 2, giving the x coordinates range.
ylim

numeric vector of length 2, giving the y coordinates range.
main

an overall title for the plot: see 'title'.
sub

a sub title for the plot: see 'title'.
col

color code or name, see 'par'.
asp

the y/x aspect ratio, see 'plot.window'.
lwd

line width for drawing symbols see 'par'.
axes

a logical value indicating whether both axes should be drawn on the plot.

Examples

plotheights(acealanme3d)

Print minimum and maximum of 3D free energy surface

Description

'print.fes3d' prints dimensionality, minimum and maximum of free energy in a fes object

Usage

## S3 method for class 'fes3d'
print(x, ...)

Arguments

x

fes3d object
...

further arguments passed to or from other methods.

Examples

tfes<-fes(acealanme3d, imax=5000)
tfes

Print hillsfile3d

Description

'print.hillsfile3d' prints dimensionality and size of a hillsfile object.

Usage

## S3 method for class 'hillsfile3d'
print(x, ...)

Arguments

x

hillsfile3d object.
...

further arguments passed to or from other methods.

Examples

acealanme3d

Print minima3d object

Description

'print.minima3d' prints 3D free energy minima (identifier, values of bins and collective variables and free energy).

Usage

## S3 method for class 'minima3d'
print(x, ...)

Arguments

x

minima object.
...

further arguments passed to or from other methods.

Examples

tfes<-fes(acealanme3d, imax=5000)
minima<-fesminima(tfes)
minima

Read 3D HILLS from Plumed

Description

'read.hills3d' reads a HILLS file generated by Plumed and returns a hillsfile3d object. User can specify whether some collective variables are periodic.

Usage

read.hills3d(file = "HILLS", per = c(FALSE, FALSE, FALSE),
  pcv1 = c(-pi, pi), pcv2 = c(-pi, pi), pcv3 = c(-pi, pi),
  ignoretime = FALSE)

Arguments

file

HILLS file from Plumed.
per

logical vector specifying periodicity of collective variables.
pcv1

periodicity of CV1.
pcv2

periodicity of CV2.
pcv3

periodicity of CV3.
ignoretime

time in the first column of the HILLS file will be ignored.

Value

hillsfile object.

Examples

l1<-"1 -1.587 -2.969  3.013 0.3 0.3 0.3 1.111 10"
l2<-"2 -1.067  2.745  2.944 0.3 0.3 0.3 1.109 10"
l3<-"3 -1.376  2.697  3.049 0.3 0.3 0.3 1.080 10"
l4<-"4 -1.663  2.922 -3.065 0.3 0.3 0.3 1.072 10"
fourhills<-c(l1,l2,l3,l4)
tf <- tempfile()
writeLines(fourhills, tf)
read.hills3d(tf, per=c(TRUE,TRUE))

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))

Print summary of 3D free energy surface

Description

'summary.fes3d' prints minimum and maximum of free energy in a fes object.

Usage

## S3 method for class 'fes3d'
summary(object, ...)

Arguments

object

fes3d object.
...

further arguments passed to or from other methods.

Examples

tfes<-fes(acealanme3d, imax=5000)
summary(tfes)

Print summary for hillsfile3d

Description

'summary.hillsfile3d' prints dimensionality, size and collective variable ranges of a hillsfile3d object.

Usage

## S3 method for class 'hillsfile3d'
summary(object, ...)

Arguments

object

hillsfile3d object.
...

further arguments passed to or from other methods.

Examples

summary(acealanme3d)

Print minima3d object summary

Description

'summary.minima3d' prints summary for 3D free energy minima (identifier, values of bins and collective variables, free energy and equilibrium populations).

Usage

## S3 method for class 'minima3d'
summary(object, temp = 300, eunit = "kJ/mol", ...)

Arguments

object

minima3d object
temp

temperature in Kelvins
eunit

energy units (kJ/mol or kcal/mol, kJ/mol is default)
...

further arguments passed to or from other methods.

Examples

tfes<-fes(acealanme3d, imax=5000)
minima<-fesminima(tfes)
summary(minima)

Print last n lines of hillsfile3d

Description

'tail.hillsfile3d' prints last n lines of a hillsfile3d object.

Usage

## S3 method for class 'hillsfile3d'
tail(x, n = 10, ...)

Arguments

x

hillsfile3d object.
n

number of lines (default 10).
...

further arguments passed to or from other methods.

Examples

tail(acealanme3d)