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Commit e8891fad authored by Massimiliano Bonomi's avatar Massimiliano Bonomi
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user-doc/tutorials/a-master-ISDD-1.txt
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View file @ e8891fad
......@@ -112,7 +112,7 @@ whose value is specified. Action names are highlighted in green and, clicking on
corresponding page in the manual that contains a detailed description for each keyword.
Actions that support the keyword `STRIDE` are those that determine how frequently things are to be done.
Notice that the default value for `STRIDE` is always 1. In the example above, omitting `STRIDE` keywords
the corresponding COLVAR files would have been written for every frame of the analyzed trajectory.
the corresponding `COLVAR` files would have been written for every frame of the analyzed trajectory.
All the other actions in the example above do not
support the `STRIDE` keyword and are only calculated when requested. That is, `d` will be computed
every 10 frames, and `phi1` and `phi2` every 100 frames.
......@@ -156,9 +156,9 @@ wget https://github.com/plumed/lugano2019/raw/master/handson_1/handson_1.tgz
\endverbatim
The archive contains the following files:
- GB1_native.pdb : A PDB file with the native structure of the GB1 protein.
- traj-whole.xtc: A trajectory in xtc format. To make the exercise easier, GB1 has been made whole already.
- traj-broken.xtc: The same trajectory as it was originally produced by GROMACS. Here GB1 is broken by periodic boundary conditions and should be fixed.
- `GB1_native.pdb` : A PDB file with the native structure of the GB1 protein.
- `traj-whole.xtc` : A trajectory in `xtc` format. To make the exercise easier, GB1 has been made whole already.
- `traj-broken.xtc` : The same trajectory as it was originally produced by GROMACS. Here GB1 is broken by periodic boundary conditions and should be fixed.
The archive can be unpacked using the following command:
......@@ -174,12 +174,11 @@ This tutorial has been tested with PLUMED version 2.6.2.
In this exercise, we will make practice with computing and printing collective variables.
To analyze the trajectories provided here, you should:
- Create a PLUMED input file with a text editor (let us call it `plumed.dat`) similar to the one above.
- Run the command `plumed driver` command (see below)
- Create a PLUMED input file with a text editor (let us call it `plumed.dat`) similar to the one above;
- Run the command `plumed driver` (see below).
Notice that you can also visualize trajectories with VMD directly.
For example, the trajectory `traj-whole.xtc` can be visualized with
the command:
For example, the trajectory `traj-whole.xtc` can be visualized with the command:
\verbatim
vmd GB1_native.pdb traj-whole.xtc
......@@ -258,7 +257,7 @@ the dihedral phi is defined by these atoms: C(i-1),N(i),CA(i),C(i) (see Fig. \re
\anchor master-ISDD-1-dih-fig
\image html master-ISDD-1-dih-fig.png "Definition of backbone dihedral angles phi and psi."
After consulting the manual and inspecting GB1_native.pdb, let's define the dihedral angle phi of residue 2
After consulting the manual and inspecting `GB1_native.pdb`, let's define the dihedral angle phi of residue 2
in two different ways: using the \ref MOLINFO shortcut and with an explicit list of 4 atoms.
\plumedfile
......@@ -304,16 +303,16 @@ PRINT ARG=d1,d2 STRIDE=1 FILE=COLVAR
The file above instructs PLUMED to:
1. calculate the position of the Virtual Atom 'first' as the \ref CENTER of atoms from 1 to 8;
2. calculate the position of the Virtual Atom 'last' as the \ref CENTER of atoms from 427 to 436;
3. calculate the distance between the two Virtual Atoms 'first' and 'last' and saves it in 'd1';
4. calculate the distance (ignoring periodic boundary conditions) between the two Virtual Atom 'first' and 'last' and saves it in 'd2';
5. print the content of 'd1' and 'd2' in the file COLVAR for every frame of the trajectory
1. calculate the position of the virtual atom `first` as the \ref CENTER of atoms from 1 to 8;
2. calculate the position of the virtual atom `last` as the \ref CENTER of atoms from 427 to 436;
3. calculate the distance between the two virtual atoms `first` and `last` and saves it in `d1`;
4. calculate the distance (ignoring periodic boundary conditions) between the two virtual atom `first` and `last` and saves it in `d2`;
5. print the content of `d1` and `d2` in the file `COLVAR` for every frame of the trajectory
Notice that in the input above we have used two different ways of writing the atoms used in the \ref CENTER calculation:
1. ATOMS=1,2,3,4,5,6,7,8 is the explicit list of the atoms we need
2. ATOMS=427-436 is the range of atoms needed
1. `ATOMS=1,2,3,4,5,6,7,8` is the explicit list of the atoms we need
2. `ATOMS=427-436` is the range of atoms needed
Once you have prepared a PLUMED input file containing the above instructions, you can execute it on the trajectory `traj-broken.xtc`
by making use of the following command:
......
user-doc/tutorials/a-master-ISDD-2.txt
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......@@ -163,18 +163,18 @@ PRINT ARG=__FILL__ FILE=COLVAR STRIDE=10
\endplumedfile
The syntax for the command \ref METAD is simple.
The directive is followed by a keyword ARG followed by the labels of the CVs
The directive is followed by a keyword `ARG` followed by the labels of the CVs
on which the metadynamics potential will act.
The keyword PACE determines the stride of Gaussian deposition in number of time steps,
while the keyword HEIGHT specifies the height of the Gaussian in kJ/mol. For each CVs, one has
to specify the width of the Gaussian by using the keyword SIGMA. Gaussian will be written
to the file indicated by the keyword FILE.
In this example, the bias potential will be stored on a grid, whose boundaries are specified by the keywords GRID_MIN and GRID_MAX.
Notice that you can provide either the number of bins for every collective variable (GRID_BIN) or
the desired grid spacing (GRID_SPACING). In case you provide both PLUMED will use
The keyword `PACE` determines the stride of Gaussian deposition in number of time steps,
while the keyword `HEIGHT` specifies the height of the Gaussian in kJ/mol. For each CVs, one has
to specify the width of the Gaussian by using the keyword `SIGMA`. Gaussian will be written
to the file indicated by the keyword `FILE`.
In this example, the bias potential will be stored on a grid, whose boundaries are specified by the keywords `GRID_MIN` and `GRID_MAX`.
Notice that you can provide either the number of bins for every collective variable (`GRID_BIN`) or
the desired grid spacing (`GRID_SPACING`). In case you provide both PLUMED will use
the most conservative choice (highest number of bins) for each dimension.
In case you do not provide any information about bin size (neither GRID_BIN nor GRID_SPACING)
In case you do not provide any information about bin size (neither `GRID_BIN` nor `GRID_SPACING`)
and if Gaussian width is fixed, PLUMED will use 1/5 of the Gaussian width as grid spacing.
This default choice should be reasonable for most applications.
......@@ -184,10 +184,10 @@ Once your `plumed.dat` file is complete, you can run a 10-ns long metadynamics s
> gmx mdrun -s topol.tpr -nsteps 5000000 -plumed plumed.dat
\endverbatim
During the metadynamics simulation, PLUMED will create two files, named COLVAR and HILLS.
The COLVAR file contains all the information specified by the PRINT command, in this case
During the metadynamics simulation, PLUMED will create two files, named `COLVAR` and `HILLS`.
The `COLVAR` file contains all the information specified by the \ref PRINT command, in this case
the value of the CVs every 10 steps of simulation, along with the current value of the metadynamics bias potential.
We can use `gnuplot` to visualize the behavior of the CV during the simulation, as reported in the COLVAR file:
We can use `gnuplot` to visualize the behavior of the CV during the simulation, as reported in the `COLVAR` file:
\verbatim
gnuplot> p "COLVAR" u 1:2
......@@ -212,9 +212,9 @@ If we give a look at the header of this file, we can find relevant information a
#! SET max_phi pi
\endverbatim
The line starting with FIELDS tells us what is displayed in the various columns of the HILLS file:
The line starting with `FIELDS` tells us what is displayed in the various columns of the `HILLS` file:
the simulation time, the instantaneous value of \f$ \phi \f$, the Gaussian width and height, and the bias factor.
We can use the HILLS file to visualize the decrease of the Gaussian height during the simulation,
We can use the `HILLS` file to visualize the decrease of the Gaussian height during the simulation,
according to the well-tempered recipe:
\anchor master-ISDD-2-phihills-fig
......@@ -232,7 +232,7 @@ of your metadynamics simulation!
One can estimate the free energy as a function of the metadynamics CVs directly from the metadynamics
bias potential. In order to do so, the utility \ref sum_hills should be used to sum the Gaussian kernels
deposited during the simulation and stored in the HILLS file.
deposited during the simulation and stored in the `HILLS` file.
To calculate the free energy as a function of \f$ \phi \f$, it is sufficient to use the following command line:
\verbatim
......@@ -298,9 +298,9 @@ There are multiple ways to calculate the correct
statistical weight of each frame in your metadynamics trajectory and thus to reweight your simulation.
Two of these approaches are:
- Weights are calculated by considering the time-dependence of the metadynamics bias
1. Weights are calculated by considering the time-dependence of the metadynamics bias
potential \cite Tiwary_jp504920s;
- Weights are calculated using the metadynamics bias potential obtained at the end of the
2. Weights are calculated using the metadynamics bias potential obtained at the end of the
simulation and assuming a constant bias during the entire course of the simulation \cite Branduardi:2012dl.
In this exercise we will use the second method, which resembles the umbrella-sampling-like reweighting approach.
......@@ -336,7 +336,7 @@ metad: __FILL__ ARG=__FILL__ ...
PRINT ARG=phi,psi,metad.bias FILE=COLVAR_REWEIGHT STRIDE=1 # <- also change this one!
\endplumedfile
Then run the driver using this command
Then run the \ref driver using this command
\verbatim
> plumed driver --mf_xtc traj_comp.xtc --plumed plumed_reweight.dat --kt 2.494339
......
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