| Type: | Package |
| Title: | Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed' |
| Version: | 0.1.7 |
| Date: | 2022-04-12 |
| Depends: | R (≥ 3.3.0) |
| LinkingTo: | Rcpp |
| 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. 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. Transition states can be analyzed by Nudged Elastic Band method by Henkelman, G. and Jonsson, H. (2000) <doi:10.1063/1.1323224>. Free energy surfaces, minima and transition paths can be plotted to produce publication quality images. |
| LazyData: | true |
| License: | GPL-3 |
| RoxygenNote: | 6.1.0 |
| Imports: | Rcpp |
| Suggests: | testthat |
| URL: | https://metadynamics.cz/metadynminer/ |
| NeedsCompilation: | yes |
| Packaged: | 2022-04-14 10:28:16 UTC; spiwokv |
| Author: | Vojtech Spiwok 
[aut, cre] |
| Maintainer: | Vojtech Spiwok <spiwokv@vscht.cz> |
| Repository: | CRAN |
| Date/Publication: | 2022-04-14 11:02:29 UTC |
Hills from 30 ns metadynamics of AceAlaNme in water with two collective variables
Description
Hills from 30 ns metadynamics of AceAlaNme (Amber99SB-ILDN) in water (TIP3P) with Ramachandran dihedrals phi and psi as collective variables.
Usage
acealanme
Format
hillsfile object
Source
http://www.metadynamics.cz/metadynminer/data/HILLS2d
Hills from 30 ns metadynamics of AceAlaNme in water with one collective variable
Description
Hills from 30 ns metadynamics of AceAlaNme (Amber99SB-ILDN) in water (TIP3P) with a Ramachandran dihedral phi as the collective variable.
Usage
acealanme1d
Format
hillsfile object
Source
http://www.metadynamics.cz/metadynminer/data/HILLS1d
Generate empty HILLS from Plumed
Description
'emptyhills' returns a hillsfile object with no hills. User can specify whether some collective variables are periodic.
Usage
emptyhills(dim=2, per=c(FALSE, FALSE), pcv1=c(-pi,pi), pcv2=c(-pi,pi))
Arguments
dim |
dimensionality of the output. |
per |
logical vector specifying periodicity of collective variables. |
pcv1 |
periodicity of CV1. |
pcv2 |
periodicity of CV2. |
Value
hillsfile object.
Examples
emptyhills(dim=2)
Calculate free energy profile for minima object (generic function for 'metadynminer' and 'metadynminer3d')
Description
'feprof' 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
feprof(minims, imax)
Arguments
minims |
minima object. |
imax |
index of a hill from which summation stops (default the rest of hills). |
Calculate free energy profile for minima object
Description
'feprof.minima' 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 'minima'
feprof(minims, imax = NULL)
Arguments
minims |
minima object. |
imax |
index of a hill from which summation stops (default the rest of hills). |
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
prof<-feprof(minima)
prof
Calculate free energy surface by Bias Sum algorithm (generic function for 'metadynminer' and 'metadynminer3d')
Description
'fes' sums up hills using fast Bias Sum algorithm.
Usage
fes(hills, imin, imax, xlim, ylim, zlim, npoints)
Arguments
hills |
hillsfile 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.
Calculate free energy surface by Bias Sum algorithm
Description
'fes.hillsfile' sums up hills using fast Bias Sum algorithm.
Usage
## S3 method for class 'hillsfile'
fes(hills, imin = 1, imax = NULL, xlim = NULL,
ylim = NULL, zlim = NULL, npoints = 256)
Arguments
hills |
hillsfile 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<-fes(acealanme, imax=5000)
Calculate free energy surface by conventional algorithm (generic function for 'metadynminer' and 'metadynminer3d')
Description
'fes2' sums up hills using slow conventional algorithm. It can be used as a reference or when hill widths are variable.
Usage
fes2(hills, imin, imax, xlim, ylim, zlim, npoints)
Arguments
hills |
hillsfile 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.
Calculate free energy surface by conventional algorithm
Description
'fes2.hillsfile' 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 'hillsfile'
fes2(hills, imin = 1, imax = NULL, xlim = NULL,
ylim = NULL, zlim = NULL, npoints = 256)
Arguments
hills |
hillsfile 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(acealanme, imax=1000)
Calculate 1D free energy surface from hillsfile object
Description
'fes2d21d' calculates 2D free energy surface, converts free energies to probabilities (exp(-F/kT)), sums them up along one collective variable and converts back to free energy (-kT log(P)).
Usage
fes2d21d(hills, remdim = 2, temp = 300, eunit = "kJ/mol", imin = 1,
imax = NULL, xlim = NULL, ylim = NULL, npoints = 256)
Arguments
hills |
hillsfile object. |
remdim |
dimension to be removed (1 for CV1, 2 for CV2, default 2). |
temp |
temperature in Kelvins (default 300). |
eunit |
energy units (kJ/mol or kcal/mol, kJ/mol is default). |
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. |
npoints |
resolution of the free energy surface in number of points. |
Value
fes object.
Examples
tfes<-fes2d21d(acealanme, remdim=2, imax=5000)
Find free energy minima in the fes object (generic function for 'metadynminer' and 'metadynminer3d')
Description
'fesminima' finds free energy minima on 1D or 2D free energy surface. The surface is divided by a 1D or 2D 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
fesminima(inputfes, nbins)
Arguments
inputfes |
fes object. |
nbins |
number of bins for each CV (default 8). |
Value
minima object.
Find free energy minima in the fes object
Description
'fesminima.fes' finds free energy minima on 1D or 2D free energy surface. The surface is divided by a 1D or 2D 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 'fes'
fesminima(inputfes, nbins = 8)
Arguments
inputfes |
fes object. |
nbins |
number of bins for each CV (default 8). |
Value
minima object.
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
minima
Calculate free energy at given point in the CV space (generic function for 'metadynminer' and 'metadynminer3d')
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
fespoint(hills, coord, imin, imax, verb)
Arguments
hills |
hillsfile 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). |
Calculate free energy at given point in the CV space
Description
‘fespoint.hillsfile' 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 'hillsfile'
fespoint(hills, coord = NULL, imin = 1,
imax = NULL, verb = T)
Arguments
hills |
hillsfile 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(acealanme, c(0,0), imax=5000)
Print first n lines of hillsfile
Description
'head.hillsfile' prints first n lines of a hillsfile object.
Usage
## S3 method for class 'hillsfile'
head(x, n = 10, ...)
Arguments
x |
hillsfile object. |
n |
number of lines (default 10). |
... |
further arguments passed to or from other methods. |
Examples
head(acealanme)
Plots 1D free energy surface object as lines
Description
'lines.fes' plots 1D free energy surface as lines.
Usage
## S3 method for class 'fes'
lines(x, lwd = 1, col = "black", ...)
Arguments
x |
fes object. |
lwd |
line width for drawing symbols see 'par'. |
col |
color code or name, see 'par'. |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme1d, imax=5000)
plot(tfes)
lines(tfes, lwd=4)
Plot lines for hillsfile object
Description
'lines.hillsfile' plots lines for hillsfile object. For a hillsfile with one collective variable it plots its evolution. For a hillsfile with two collective variables it plots CV1 vs. CV2.
Usage
## S3 method for class 'hillsfile'
lines(x, ignoretime = FALSE, lwd = 1,
col = "black", ...)
Arguments
x |
hillsfile object. |
ignoretime |
time in the first column of the HILLS file will be ignored. |
lwd |
line width for drawing symbols see 'par'. |
col |
color code or name, see 'par'. |
... |
further arguments passed to or from other methods. |
Examples
plot(acealanme)
lines(acealanme, col="red")
Plot lines for Nudged Elastic Band
Description
'lines.nebpath' plots lines for free energy profile calculated by Nudged Elastic Band.
Usage
## S3 method for class 'nebpath'
lines(x, col = "red", lwd = 1, ...)
Arguments
x |
nebpath object. |
col |
color code or name, see 'par'. |
lwd |
line width for drawing symbols see 'par'. |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
nebAD<-neb(minima, min1="A", min2="D", nsteps=20)
plot(nebAD)
lines(nebAD, lwd=4)
Plot lines for Nudged Elastic Band projected onto free energy surface
Description
'linesonfes' plots lines for free energy profile calculated by Nudged Elastic Band projected onto free energy surface.
Usage
linesonfes(x, col = "red", lwd = 1)
Arguments
x |
nebpath object. |
col |
color code or name, see 'par'. |
lwd |
line width for drawing symbols see 'par'. |
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
nebAD<-neb(minima, min1="A", min2="D", nsteps=20)
plot(minima)
linesonfes(nebAD)
Calculate maximum of free energy surface
Description
'max.fes' calculates maximum of free energy in a fes object.
Usage
## S3 method for class 'fes'
max(inputfes, na.rm = NULL, ...)
Arguments
inputfes |
fes object. |
na.rm |
a logical indicating whether missing values should be removed. |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
max(tfes)
Calculate minimum of free energy surface
Description
'min.fes' calculates minimum of free energy in a fes object.
Usage
## S3 method for class 'fes'
min(inputfes, na.rm = NULL, ...)
Arguments
inputfes |
fes object. |
na.rm |
a logical indicating whether missing values should be removed. |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
min(tfes)
Find transition path on free energy surface by Nudged Elastic Band method
Description
'neb' finds a transition path on free energy surface for a given pair of minima. For a 1D surface it simply takes the free energy profile between the two minima. For 2D surface it calculates the transition path by Nudged Elastic
Usage
neb(minims = minims, min1 = "A", min2 = "B", nbins = 20,
nsteps = 100, step = 1, k = 0.2)
Arguments
minims |
minima object. |
min1 |
starting minimum identifier (can be letter or index, default "A"). |
min2 |
final minimum identifier (can be letter or index, default "B"). |
nbins |
number of bins along Nudged Elastic Band (default 20). |
nsteps |
number of Nudged Elastic Band iterations (default 100). |
step |
Nudged Elastic Band iteration step (default 1). |
k |
Nudged Elastic Band toughness (default 0.2). |
Value
NEB path
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
nebAD<-neb(minima, min1="A", min2="D", nsteps=20)
nebAD
Creates one ad hoc free energy minimum for a fes object (generic function for 'metadynminer' and 'metadynminer3d')
Description
'oneminimum' creates an ad hoc free energy minimum on free energy surface. This can be used to calculate free energy surface evolution at arbitrary point of free energy surface.
Usage
oneminimum(inputfes, cv1, cv2, cv3)
Arguments
inputfes |
fes 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.
Creates one ad hoc free energy minimum for a fes object
Description
'oneminimum.fes' creates an ad hoc free energy minimum on free energy surface. This can be used to calculate free energy surface evolution at arbitrary point of free energy surface.
Usage
## S3 method for class 'fes'
oneminimum(inputfes, cv1, cv2, cv3)
Arguments
inputfes |
fes 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(acealanme1d)
minima<-fesminima(tfes)
minima<-minima+oneminimum(tfes, cv1=0, cv2=0)
minima
Plot free energy surface object
Description
'plot.fes' plots free energy surface. For a fes with one collective variable it plots a 1D profile. For a fes with two collective variables it plots 2D free energy surface using image, contours or combination of both (default).
Usage
## S3 method for class 'fes'
plot(x, plottype = "both", colscale = F, xlim = NULL,
ylim = NULL, zlim = NULL, main = NULL, sub = NULL, xlab = NULL,
ylab = NULL, nlevels = 10, levels = NULL,
col = rainbow(135)[100:1], labels = NULL, labcex = 0.6,
drawlabels = TRUE, colscalelab = "free energy",
method = "flattest", contcol = par("fg"), lty = par("lty"),
lwd = 1, asp = NULL, axes = T, ...)
Arguments
x |
fes object. |
plottype |
specifies whether 2D free energy surface will be plotted as image, contours or both (default "both"). |
colscale |
specifies whether color scale will be plotted (default False). |
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'. |
xlab |
a title for the x axis: see 'title'. |
ylab |
a title for the y axis: see 'title'. |
nlevels |
number of contour levels desired if 'levels' is not supplied. |
levels |
numeric vector of levels at which to draw contour lines. |
col |
color of the free energy surface. For 1D surface it is the color of the line. For 2D it is a list of colors such as that generated by 'rainbow', 'heat.colors', 'topo.colors', 'terrain.colors' or similar functions (default=rainbow(135)[100:1]). |
labels |
a vector giving the labels for the contour lines. If 'NULL' then the levels are used as labels, otherwise this is coerced by 'as.character'. |
labcex |
'cex' for contour labeling. This is an absolute size, not a multiple of 'par("cex")'. |
drawlabels |
logical. Contours are labeled if 'TRUE'. |
colscalelab |
color scale label (default "free energy"). |
method |
character string specifying where the labels will be located. Possible values are '"simple"', '"edge"' and '"flattest"' (the default). See the 'Details' section. |
contcol |
contour color. |
lty |
line type for the lines drawn. |
lwd |
contour line width. |
asp |
the y/x aspect ratio, see 'plot.window'. |
axes |
a logical value indicating whether both axes should be drawn on the plot. |
... |
further arguments passed to or from other methods. |
Examples
tfes2d<-fes(acealanme, imax=5000)
plot(tfes2d)
tfes1d<-fes(acealanme1d)
plot(tfes1d)
Plot hillsfile object
Description
'plot.hillsfile' plots hillsfile object. For a hillsfile with one collective variable it plots its evolution. For a hillsfile with two collective variables it plots CV1 vs. CV2.
Usage
## S3 method for class 'hillsfile'
plot(x, ignoretime = FALSE, xlab = NULL,
ylab = NULL, xlim = NULL, ylim = NULL, main = NULL, sub = NULL,
pch = 1, col = "black", bg = "red", cex = 1, asp = NULL,
lwd = 1, axes = TRUE, ...)
Arguments
x |
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'. |
pch |
plotting 'character', i.e., symbol to use. See 'points'. |
col |
color code or name, see 'par'. |
bg |
background (fill) color for the open plot symbols given by 'pch = 21:25'. |
cex |
character (or symbol) expansion: a numerical vector. This works as a multiple of 'par("cex")'. |
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. |
... |
further arguments passed to or from other methods. |
Examples
plot(acealanme)
Plot minima object
Description
'plot.minima' plots free energy surface with minima. The free energy surface is plotted the same way as by plot.fes with additional minima labels.
Usage
## S3 method for class 'minima'
plot(x, plottype = "both", xlim = NULL, ylim = NULL,
zlim = NULL, colscale = F, colscalelab = "free energy",
main = NULL, sub = NULL, xlab = NULL, ylab = NULL,
nlevels = 10, levels = NULL, col = rainbow(135)[100:1],
labels = NULL, labcex = 0.6, drawlabels = TRUE,
method = "flattest", textcol = "black", pch = 1, bg = "red",
cex = 1, contcol = par("fg"), lty = par("lty"), lwd = par("lwd"),
asp = NULL, axes = TRUE, ...)
Arguments
x |
minima object. |
plottype |
specifies whether 2D free energy surface will be plotted as image, contours or both (default "both"). |
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. |
colscale |
specifies whether color scale will be plotted (default False). |
colscalelab |
color scale label (default "free energy"). |
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'. |
nlevels |
number of contour levels desired if 'levels' is not supplied. |
levels |
numeric vector of levels at which to draw contour lines. |
col |
color of the free energy surface. For 1D surface it is the color of the line. For 2D it is a list of colors such as that generated by 'rainbow', 'heat.colors', 'topo.colors', 'terrain.colors' or similar functions (default=rainbow(135)[100:1]). |
labels |
a vector giving the labels for the contour lines. If 'NULL' then the levels are used as labels, otherwise this is coerced by 'as.character'. |
labcex |
'cex' for contour labeling. This is an absolute size, not a multiple of 'par("cex")'. |
drawlabels |
logical. Contours are labeled if 'TRUE'. |
method |
character string specifying where the labels will be located. Possible values are '"simple"', '"edge"' and '"flattest"' (the default). See the 'Details' section. |
textcol |
color of minima labels. |
pch |
plotting 'character', i.e., symbol to use. See 'points' |
bg |
background (fill) color for the open plot symbols given by 'pch = 21:25'. |
cex |
character (or symbol) expansion: a numerical vector. This works as a multiple of 'par("cex")'. |
contcol |
contour color. |
lty |
line type for the lines drawn. |
lwd |
contour line width. |
asp |
the y/x aspect ratio, see 'plot.window'. |
axes |
a logical value indicating whether both axes should be drawn on the plot. |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
plot(minima)
Plot Nudged Elastic Band
Description
'plot.nebpath' plots free energy profile calculated by Nudged Elastic Band.
Usage
## S3 method for class 'nebpath'
plot(x, xlim = NULL, ylim = NULL, main = NULL,
sub = NULL, xlab = "bin", ylab = "free energy", col = "red",
lwd = 1, asp = NULL, cex = 1, axes = T, ...)
Arguments
x |
nebpath object. |
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'. |
xlab |
a title for the x axis: see 'title'. |
ylab |
a title for the y axis: see 'title'. |
col |
color code or name, see 'par'. |
lwd |
line width for drawing symbols see 'par'. |
asp |
the y/x aspect ratio, see 'plot.window'. |
cex |
text expansion. |
axes |
a logical value indicating whether both axes should be drawn on the plot. |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
nebAD<-neb(minima, min1="A", min2="D", nsteps=20)
plot(nebAD)
Plot free energy profile
Description
'plot.profiles' plots evolution of free energy differences between minima. They are colored by rainbow colors from the global one (blue) to the highest (red).
Usage
## S3 method for class 'profiles'
plot(x, which = NULL, ignoretime = FALSE,
xlim = NULL, ylim = NULL, main = NULL, sub = NULL, xlab = NULL,
ylab = NULL, col = NULL, asp = NULL, lwd = 1, axes = T, ...)
Arguments
x |
profiles object. |
which |
vector of indexes of profiles to be plotted (default all). |
ignoretime |
time in the first column of the HILLS file will be ignored. |
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'. |
xlab |
a title for the x axis: see 'title'. |
ylab |
a title for the y axis: see 'title'. |
col |
color code or name, see 'par'. |
asp |
the y/x aspect ratio, see 'plot.window'. |
lwd |
line width. |
axes |
a logical value indicating whether both axes should be drawn on the plot. |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
prof<-feprof(minima)
plot(prof)
Plot evolution of heights of hills (generic function for 'metadynminer' and 'metadynminer3d')
Description
'plotheights' 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
plotheights(hills, ignoretime, xlab, ylab, xlim, ylim, main, sub, col, asp,
lwd, axes)
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. |
Plot evolution of heights of hills in hillsfile object
Description
'plotheights.hillsfile' 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 'hillsfile'
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(acealanme)
Plots 1D free energy surface object as points
Description
'points.fes' plots 1D free energy surface as points.
Usage
## S3 method for class 'fes'
points(x, pch = 1, col = "black", bg = "red",
cex = 1, lwd = 1, ...)
Arguments
x |
fes object. |
pch |
plotting 'character', i.e., symbol to use. See 'points' |
col |
color code or name, see 'par'. |
bg |
background (fill) color for the open plot symbols given by 'pch = 21:25'. |
cex |
character (or symbol) expansion: a numerical vector. This works as a multiple of 'par("cex")'. |
lwd |
line width for drawing symbols see 'par'. |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme1d, imax=5000)
plot(tfes)
points(tfes)
Plot points for hillsfile object
Description
'points.hillsfile' plots points for hillsfile object. For a hillsfile with one collective variable it plots its evolution. For a hillsfile with two collective variables it plots CV1 vs. CV2.
Usage
## S3 method for class 'hillsfile'
points(x, ignoretime = FALSE, pch = 1,
col = "black", bg = "red", cex = 1, lwd = 1, ...)
Arguments
x |
hillsfile object. |
ignoretime |
time in the first column of the HILLS file will be ignored. |
pch |
plotting 'character', i.e., symbol to use. See 'points'. |
col |
color code or name, see 'par'. |
bg |
background (fill) color for the open plot symbols given by 'pch = 21:25'. |
cex |
character (or symbol) expansion: a numerical vector. This works as a multiple of 'par("cex")'. |
lwd |
line width for drawing symbols see 'par'. |
... |
further arguments passed to or from other methods. |
Examples
plot(acealanme)
points(acealanme, col="red")
Plot points for Nudged Elastic Band
Description
'points.nebpath' plots points for free energy profile calculated by Nudged Elastic Band.
Usage
## S3 method for class 'nebpath'
points(x, pch = NULL, cex = 1, bg = NULL,
col = "red", lwd = 1, ...)
Arguments
x |
nebpath object. |
pch |
plotting 'character', i.e., symbol to use. See 'points'. |
cex |
character (or symbol) expansion: a numerical vector. This works as a multiple of 'par("cex")'. |
bg |
background (fill) color for the open plot symbols given by 'pch = 21:25'. |
col |
color code or name, see 'par'. |
lwd |
line width for drawing symbols see 'par'. |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
nebAD<-neb(minima, min1="A", min2="D", nsteps=20)
plot(nebAD)
points(nebAD)
Plot points for Nudged Elastic Band projected onto free energy surface
Description
'pointsonfes' plots points for free energy profile calculated by Nudged Elastic Band projected onto free energy surface.
Usage
pointsonfes(x, pch = NULL, cex = 1, bg = NULL, col = "red",
lwd = 1)
Arguments
x |
nebpath object. |
pch |
plotting 'character', i.e., symbol to use. See 'points'. |
cex |
character (or symbol) expansion: a numerical vector. This works as a multiple of 'par("cex")'. |
bg |
background (fill) color for the open plot symbols given by 'pch = 21:25'. |
col |
color code or name, see 'par'. |
lwd |
line width for drawing symbols see 'par'. |
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
nebAD<-neb(minima, min1="A", min2="D", nsteps=20)
plot(minima)
pointsonfes(nebAD)
Print dimensionality, minimum and maximum of free energy surface
Description
'print.fes' prints dimensionality, minimum and maximum of free energy in a fes object
Usage
## S3 method for class 'fes'
print(x, ...)
Arguments
x |
fes object |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
tfes
Print hillsfile
Description
'print.hillsfile' prints dimensionality and size of a hillsfile object.
Usage
## S3 method for class 'hillsfile'
print(x, ...)
Arguments
x |
hillsfile object. |
... |
further arguments passed to or from other methods. |
Examples
acealanme
Print minima object
Description
'print.minima' prints free energy minima (identifier, values of bins and collective variables and free energy).
Usage
## S3 method for class 'minima'
print(x, ...)
Arguments
x |
minima object. |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
minima
Print Nudged Elastic Band minima
Description
'print.nebpath' prints the list minima for Nudged Elastic Band
Usage
## S3 method for class 'nebpath'
print(x, ...)
Arguments
x |
nebpath object |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
nebAD<-neb(minima, min1="A", min2="D", nsteps=20)
nebAD
Print profiles object
Description
'print.profiles' prints free energy profile.
Usage
## S3 method for class 'profiles'
print(x, ...)
Arguments
x |
minima object. |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
prof<-feprof(minima)
prof
Calculate probability of free energy surface
Description
'prob' calculates probability from free energy in a fes object.
Usage
prob(inputfes, temp = 300, eunit = "kJ/mol")
Arguments
inputfes |
fes object. |
temp |
temperature in Kelvins. |
eunit |
energy units (kJ/mol or kcal/mol, kJ/mol is default). |
Examples
tfes<-fes(acealanme, imax=5000)
print(prob(tfes))
Read HILLS from Plumed
Description
'read.hills' reads a HILLS file generated by Plumed and returns a hillsfile object. User can specify whether some collective variables are periodic.
Usage
read.hills(file = "HILLS", per = c(FALSE, FALSE), pcv1 = c(-pi, pi),
pcv2 = 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. |
ignoretime |
time in the first column of the HILLS file will be ignored. |
Value
hillsfile object.
Examples
l1<-"1 -1.409 2.808 0.3 0.3 1.111 10"
l2<-"2 -2.505 2.791 0.3 0.3 1.111 10"
l3<-"3 -2.346 2.754 0.3 0.3 1.069 10"
l4<-"4 -1.198 2.872 0.3 0.3 1.074 10"
fourhills<-c(l1,l2,l3,l4)
tf <- tempfile()
writeLines(fourhills, tf)
read.hills(tf, per=c(TRUE,TRUE))
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))
Print summary of free energy surface
Description
'summary.fes' prints dimensionality, minimum and maximum of free energy in a fes object.
Usage
## S3 method for class 'fes'
summary(object, ...)
Arguments
object |
fes object. |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
summary(tfes)
Print summary for hillsfile
Description
'summary.hillsfile' prints dimensionality, size and collective variable ranges of a hillsfile object.
Usage
## S3 method for class 'hillsfile'
summary(object, ...)
Arguments
object |
hillsfile object. |
... |
further arguments passed to or from other methods. |
Examples
summary(acealanme)
Print minima object summary
Description
'summary.minima' prints summary for free energy minima (identifier, values of bins and collective variables, free energy and equilibrium populations).
Usage
## S3 method for class 'minima'
summary(object, temp = 300, eunit = "kJ/mol", ...)
Arguments
object |
minima 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(acealanme, imax=5000)
minima<-fesminima(tfes)
summary(minima)
Print summary for Nudged Elastic Band
Description
'print.nebpath' prints the list minima for Nudged Elastic Band, activation energies and half lives calculated by Eyring equation (https://doi.org/10.1063/1.1749604).
Usage
## S3 method for class 'nebpath'
summary(object, temp = 300, eunit = "kJ/mol", ...)
Arguments
object |
nebpath 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(acealanme, imax=5000)
minima<-fesminima(tfes)
nebAD<-neb(minima, min1="A", min2="D", nsteps=20)
summary(nebAD)
Print summary for free energy profile
Description
'summary.profiles' prints the list of free energy minima with maximal and minimal free energy differences.
Usage
## S3 method for class 'profiles'
summary(object, imind = 1, imaxd = NULL, ...)
Arguments
object |
profiles object. |
imind |
index of a hill from which calculation of difference starts (default 1). |
imaxd |
index of a hill from which calculation of difference stops (default the rest of hills). |
... |
further arguments passed to or from other methods. |
Examples
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
prof<-feprof(minima)
summary(prof)
Print last n lines of hillsfile
Description
'tail.hillsfile' prints last n lines of a hillsfile object.
Usage
## S3 method for class 'hillsfile'
tail(x, n = 10, ...)
Arguments
x |
hillsfile object. |
n |
number of lines (default 10). |
... |
further arguments passed to or from other methods. |
Examples
tail(acealanme)