| Title: | Tools to Read, Analyze and Visualize Metadynamics 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. 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. |
| Authors: | Vojtech Spiwok [aut, cre] |
| Maintainer: | Vojtech Spiwok <[email protected]> |
| License: | GPL-3 |
| Version: | 0.1.7 |
| Built: | 2025-02-28 03:00:42 UTC |
| Source: | https://github.com/spiwokv/metadynminer |
Hills from 30 ns metadynamics of AceAlaNme (Amber99SB-ILDN) in water (TIP3P) with Ramachandran dihedrals phi and psi as collective variables.
acealanmeacealanme
hillsfile object
http://www.metadynamics.cz/metadynminer/data/HILLS2d
Hills from 30 ns metadynamics of AceAlaNme (Amber99SB-ILDN) in water (TIP3P) with a Ramachandran dihedral phi as the collective variable.
acealanme1dacealanme1d
hillsfile object
http://www.metadynamics.cz/metadynminer/data/HILLS1d
'emptyhills' returns a hillsfile object with no hills. User can specify whether some collective variables are periodic.
emptyhills(dim=2, per=c(FALSE, FALSE), pcv1=c(-pi,pi), pcv2=c(-pi,pi))emptyhills(dim=2, per=c(FALSE, FALSE), pcv1=c(-pi,pi), pcv2=c(-pi,pi))
dim |
dimensionality of the output. |
per |
logical vector specifying periodicity of collective variables. |
pcv1 |
periodicity of CV1. |
pcv2 |
periodicity of CV2. |
hillsfile object.
emptyhills(dim=2)emptyhills(dim=2)
'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).
feprof(minims, imax)feprof(minims, imax)
minims |
minima object. |
imax |
index of a hill from which summation stops (default the rest of hills). |
'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).
## S3 method for class 'minima' feprof(minims, imax = NULL)## S3 method for class 'minima' feprof(minims, imax = NULL)
minims |
minima object. |
imax |
index of a hill from which summation stops (default the rest of hills). |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) prof<-feprof(minima) proftfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) prof<-feprof(minima) prof
'fes' sums up hills using fast Bias Sum algorithm.
fes(hills, imin, imax, xlim, ylim, zlim, npoints)fes(hills, imin, imax, xlim, ylim, zlim, npoints)
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. |
fes object.
'fes.hillsfile' sums up hills using fast Bias Sum algorithm.
## S3 method for class 'hillsfile' fes(hills, imin = 1, imax = NULL, xlim = NULL, ylim = NULL, zlim = NULL, npoints = 256)## S3 method for class 'hillsfile' fes(hills, imin = 1, imax = NULL, xlim = NULL, ylim = NULL, zlim = NULL, npoints = 256)
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. |
fes object.
tfes<-fes(acealanme, imax=5000)tfes<-fes(acealanme, imax=5000)
'fes2' sums up hills using slow conventional algorithm. It can be used as a reference or when hill widths are variable.
fes2(hills, imin, imax, xlim, ylim, zlim, npoints)fes2(hills, imin, imax, xlim, ylim, zlim, npoints)
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. |
fes object.
'fes2.hillsfile' sums up hills using slow conventional algorithm. It can be used as a reference or when hill widths are variable.
## S3 method for class 'hillsfile' fes2(hills, imin = 1, imax = NULL, xlim = NULL, ylim = NULL, zlim = NULL, npoints = 256)## S3 method for class 'hillsfile' fes2(hills, imin = 1, imax = NULL, xlim = NULL, ylim = NULL, zlim = NULL, npoints = 256)
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. |
fes object.
tfes<-fes2(acealanme, imax=1000)tfes<-fes2(acealanme, imax=1000)
'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)).
fes2d21d(hills, remdim = 2, temp = 300, eunit = "kJ/mol", imin = 1, imax = NULL, xlim = NULL, ylim = NULL, npoints = 256)fes2d21d(hills, remdim = 2, temp = 300, eunit = "kJ/mol", imin = 1, imax = NULL, xlim = NULL, ylim = NULL, npoints = 256)
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. |
fes object.
tfes<-fes2d21d(acealanme, remdim=2, imax=5000)tfes<-fes2d21d(acealanme, remdim=2, imax=5000)
'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.
fesminima(inputfes, nbins)fesminima(inputfes, nbins)
inputfes |
fes object. |
nbins |
number of bins for each CV (default 8). |
minima object.
'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.
## S3 method for class 'fes' fesminima(inputfes, nbins = 8)## S3 method for class 'fes' fesminima(inputfes, nbins = 8)
inputfes |
fes object. |
nbins |
number of bins for each CV (default 8). |
minima object.
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) minimatfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) minima
‘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.
fespoint(hills, coord, imin, imax, verb)fespoint(hills, coord, imin, imax, verb)
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). |
‘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.
## S3 method for class 'hillsfile' fespoint(hills, coord = NULL, imin = 1, imax = NULL, verb = T)## S3 method for class 'hillsfile' fespoint(hills, coord = NULL, imin = 1, imax = NULL, verb = T)
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). |
fespoint(acealanme, c(0,0), imax=5000)fespoint(acealanme, c(0,0), imax=5000)
'head.hillsfile' prints first n lines of a hillsfile object.
## S3 method for class 'hillsfile' head(x, n = 10, ...)## S3 method for class 'hillsfile' head(x, n = 10, ...)
x |
hillsfile object. |
n |
number of lines (default 10). |
... |
further arguments passed to or from other methods. |
head(acealanme)head(acealanme)
'lines.fes' plots 1D free energy surface as lines.
## S3 method for class 'fes' lines(x, lwd = 1, col = "black", ...)## S3 method for class 'fes' lines(x, lwd = 1, col = "black", ...)
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. |
tfes<-fes(acealanme1d, imax=5000) plot(tfes) lines(tfes, lwd=4)tfes<-fes(acealanme1d, imax=5000) plot(tfes) lines(tfes, lwd=4)
'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.
## S3 method for class 'hillsfile' lines(x, ignoretime = FALSE, lwd = 1, col = "black", ...)## S3 method for class 'hillsfile' lines(x, ignoretime = FALSE, lwd = 1, col = "black", ...)
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. |
plot(acealanme) lines(acealanme, col="red")plot(acealanme) lines(acealanme, col="red")
'lines.nebpath' plots lines for free energy profile calculated by Nudged Elastic Band.
## S3 method for class 'nebpath' lines(x, col = "red", lwd = 1, ...)## S3 method for class 'nebpath' lines(x, col = "red", lwd = 1, ...)
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. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) plot(nebAD) lines(nebAD, lwd=4)tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) plot(nebAD) lines(nebAD, lwd=4)
'linesonfes' plots lines for free energy profile calculated by Nudged Elastic Band projected onto free energy surface.
linesonfes(x, col = "red", lwd = 1)linesonfes(x, col = "red", lwd = 1)
x |
nebpath object. |
col |
color code or name, see 'par'. |
lwd |
line width for drawing symbols see 'par'. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) plot(minima) linesonfes(nebAD)tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) plot(minima) linesonfes(nebAD)
'max.fes' calculates maximum of free energy in a fes object.
## S3 method for class 'fes' max(inputfes, na.rm = NULL, ...)## S3 method for class 'fes' max(inputfes, na.rm = NULL, ...)
inputfes |
fes object. |
na.rm |
a logical indicating whether missing values should be removed. |
... |
further arguments passed to or from other methods. |
tfes<-fes(acealanme, imax=5000) max(tfes)tfes<-fes(acealanme, imax=5000) max(tfes)
'min.fes' calculates minimum of free energy in a fes object.
## S3 method for class 'fes' min(inputfes, na.rm = NULL, ...)## S3 method for class 'fes' min(inputfes, na.rm = NULL, ...)
inputfes |
fes object. |
na.rm |
a logical indicating whether missing values should be removed. |
... |
further arguments passed to or from other methods. |
tfes<-fes(acealanme, imax=5000) min(tfes)tfes<-fes(acealanme, imax=5000) min(tfes)
'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
neb(minims = minims, min1 = "A", min2 = "B", nbins = 20, nsteps = 100, step = 1, k = 0.2)neb(minims = minims, min1 = "A", min2 = "B", nbins = 20, nsteps = 100, step = 1, k = 0.2)
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). |
NEB path
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) nebADtfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) nebAD
'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.
oneminimum(inputfes, cv1, cv2, cv3)oneminimum(inputfes, cv1, cv2, cv3)
inputfes |
fes object. |
cv1 |
the value of collective variable 1. |
cv2 |
the value of collective variable 2. |
cv3 |
the value of collective variable 3. |
minima object.
'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.
## S3 method for class 'fes' oneminimum(inputfes, cv1, cv2, cv3)## S3 method for class 'fes' oneminimum(inputfes, cv1, cv2, cv3)
inputfes |
fes object. |
cv1 |
the value of collective variable 1. |
cv2 |
the value of collective variable 2. |
cv3 |
the value of collective variable 3. |
minima object.
tfes<-fes(acealanme1d) minima<-fesminima(tfes) minima<-minima+oneminimum(tfes, cv1=0, cv2=0) minimatfes<-fes(acealanme1d) minima<-fesminima(tfes) minima<-minima+oneminimum(tfes, cv1=0, cv2=0) minima
'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).
## 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, ...)## 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, ...)
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. |
tfes2d<-fes(acealanme, imax=5000) plot(tfes2d) tfes1d<-fes(acealanme1d) plot(tfes1d)tfes2d<-fes(acealanme, imax=5000) plot(tfes2d) tfes1d<-fes(acealanme1d) plot(tfes1d)
'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.
## 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, ...)## 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, ...)
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. |
plot(acealanme)plot(acealanme)
'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.
## 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, ...)## 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, ...)
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. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) plot(minima)tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) plot(minima)
'plot.nebpath' plots free energy profile calculated by Nudged Elastic Band.
## 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, ...)## 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, ...)
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. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) plot(nebAD)tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) plot(nebAD)
'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).
## 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, ...)## 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, ...)
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. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) prof<-feprof(minima) plot(prof)tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) prof<-feprof(minima) plot(prof)
'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.
plotheights(hills, ignoretime, xlab, ylab, xlim, ylim, main, sub, col, asp, lwd, axes)plotheights(hills, ignoretime, xlab, ylab, xlim, ylim, main, sub, col, asp, lwd, axes)
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. |
'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.
## 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)## 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)
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. |
plotheights(acealanme)plotheights(acealanme)
'points.fes' plots 1D free energy surface as points.
## S3 method for class 'fes' points(x, pch = 1, col = "black", bg = "red", cex = 1, lwd = 1, ...)## S3 method for class 'fes' points(x, pch = 1, col = "black", bg = "red", cex = 1, lwd = 1, ...)
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. |
tfes<-fes(acealanme1d, imax=5000) plot(tfes) points(tfes)tfes<-fes(acealanme1d, imax=5000) plot(tfes) points(tfes)
'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.
## S3 method for class 'hillsfile' points(x, ignoretime = FALSE, pch = 1, col = "black", bg = "red", cex = 1, lwd = 1, ...)## S3 method for class 'hillsfile' points(x, ignoretime = FALSE, pch = 1, col = "black", bg = "red", cex = 1, lwd = 1, ...)
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. |
plot(acealanme) points(acealanme, col="red")plot(acealanme) points(acealanme, col="red")
'points.nebpath' plots points for free energy profile calculated by Nudged Elastic Band.
## S3 method for class 'nebpath' points(x, pch = NULL, cex = 1, bg = NULL, col = "red", lwd = 1, ...)## S3 method for class 'nebpath' points(x, pch = NULL, cex = 1, bg = NULL, col = "red", lwd = 1, ...)
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. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) plot(nebAD) points(nebAD)tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) plot(nebAD) points(nebAD)
'pointsonfes' plots points for free energy profile calculated by Nudged Elastic Band projected onto free energy surface.
pointsonfes(x, pch = NULL, cex = 1, bg = NULL, col = "red", lwd = 1)pointsonfes(x, pch = NULL, cex = 1, bg = NULL, col = "red", lwd = 1)
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'. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) plot(minima) pointsonfes(nebAD)tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) plot(minima) pointsonfes(nebAD)
'print.fes' prints dimensionality, minimum and maximum of free energy in a fes object
## S3 method for class 'fes' print(x, ...)## S3 method for class 'fes' print(x, ...)
x |
fes object |
... |
further arguments passed to or from other methods. |
tfes<-fes(acealanme, imax=5000) tfestfes<-fes(acealanme, imax=5000) tfes
'print.hillsfile' prints dimensionality and size of a hillsfile object.
## S3 method for class 'hillsfile' print(x, ...)## S3 method for class 'hillsfile' print(x, ...)
x |
hillsfile object. |
... |
further arguments passed to or from other methods. |
acealanmeacealanme
'print.minima' prints free energy minima (identifier, values of bins and collective variables and free energy).
## S3 method for class 'minima' print(x, ...)## S3 method for class 'minima' print(x, ...)
x |
minima object. |
... |
further arguments passed to or from other methods. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) minimatfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) minima
'print.nebpath' prints the list minima for Nudged Elastic Band
## S3 method for class 'nebpath' print(x, ...)## S3 method for class 'nebpath' print(x, ...)
x |
nebpath object |
... |
further arguments passed to or from other methods. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) nebADtfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) nebAD
'print.profiles' prints free energy profile.
## S3 method for class 'profiles' print(x, ...)## S3 method for class 'profiles' print(x, ...)
x |
minima object. |
... |
further arguments passed to or from other methods. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) prof<-feprof(minima) proftfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) prof<-feprof(minima) prof
'prob' calculates probability from free energy in a fes object.
prob(inputfes, temp = 300, eunit = "kJ/mol")prob(inputfes, temp = 300, eunit = "kJ/mol")
inputfes |
fes object. |
temp |
temperature in Kelvins. |
eunit |
energy units (kJ/mol or kcal/mol, kJ/mol is default). |
tfes<-fes(acealanme, imax=5000) print(prob(tfes))tfes<-fes(acealanme, imax=5000) print(prob(tfes))
'read.hills' reads a HILLS file generated by Plumed and returns a hillsfile object. User can specify whether some collective variables are periodic.
read.hills(file = "HILLS", per = c(FALSE, FALSE), pcv1 = c(-pi, pi), pcv2 = c(-pi, pi), ignoretime = FALSE)read.hills(file = "HILLS", per = c(FALSE, FALSE), pcv1 = c(-pi, pi), pcv2 = c(-pi, pi), ignoretime = FALSE)
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. |
hillsfile object.
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))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.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.
read.plumed(file = "fes.dat", dim = 2, per = c(F, F, F))read.plumed(file = "fes.dat", dim = 2, per = c(F, F, F))
file |
input file from PLUMED sum_hills. |
per |
logical vector specifying periodicity of collective variables. |
dim |
dimension (1 or 2, default 2). |
fes object.
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))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))
'summary.fes' prints dimensionality, minimum and maximum of free energy in a fes object.
## S3 method for class 'fes' summary(object, ...)## S3 method for class 'fes' summary(object, ...)
object |
fes object. |
... |
further arguments passed to or from other methods. |
tfes<-fes(acealanme, imax=5000) summary(tfes)tfes<-fes(acealanme, imax=5000) summary(tfes)
'summary.hillsfile' prints dimensionality, size and collective variable ranges of a hillsfile object.
## S3 method for class 'hillsfile' summary(object, ...)## S3 method for class 'hillsfile' summary(object, ...)
object |
hillsfile object. |
... |
further arguments passed to or from other methods. |
summary(acealanme)summary(acealanme)
'summary.minima' prints summary for free energy minima (identifier, values of bins and collective variables, free energy and equilibrium populations).
## S3 method for class 'minima' summary(object, temp = 300, eunit = "kJ/mol", ...)## S3 method for class 'minima' summary(object, temp = 300, eunit = "kJ/mol", ...)
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. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) summary(minima)tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) summary(minima)
'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).
## S3 method for class 'nebpath' summary(object, temp = 300, eunit = "kJ/mol", ...)## S3 method for class 'nebpath' summary(object, temp = 300, eunit = "kJ/mol", ...)
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. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) summary(nebAD)tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) nebAD<-neb(minima, min1="A", min2="D", nsteps=20) summary(nebAD)
'summary.profiles' prints the list of free energy minima with maximal and minimal free energy differences.
## S3 method for class 'profiles' summary(object, imind = 1, imaxd = NULL, ...)## S3 method for class 'profiles' summary(object, imind = 1, imaxd = NULL, ...)
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. |
tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) prof<-feprof(minima) summary(prof)tfes<-fes(acealanme, imax=5000) minima<-fesminima(tfes) prof<-feprof(minima) summary(prof)
'tail.hillsfile' prints last n lines of a hillsfile object.
## S3 method for class 'hillsfile' tail(x, n = 10, ...)## S3 method for class 'hillsfile' tail(x, n = 10, ...)
x |
hillsfile object. |
n |
number of lines (default 10). |
... |
further arguments passed to or from other methods. |
tail(acealanme)tail(acealanme)