Split up analysis chapter in reference manual

[alexxy/gromacs.git] / docs / reference-manual / pulling.rst

Non-equilibrium pulling
-----------------------

When the distance between two groups is changed continuously, work is
applied to the system, which means that the system is no longer in
equilibrium. Although in the limit of very slow pulling the system is
again in equilibrium, for many systems this limit is not reachable
within reasonable computational time. However, one can use the Jarzynski
relation \ :ref:`135 <refJarzynski1997a>` to obtain the equilibrium free-energy difference
:math:`\Delta G` between two distances from many non-equilibrium
simulations:

.. math:: \Delta G_{AB} = -k_BT \log \left\langle e^{-\beta W_{AB}} \right\rangle_A
          :label: eqJarz

where :math:`W_{AB}` is the work performed to force the system along
one path from state A to B, the angular bracket denotes averaging over a
canonical ensemble of the initial state A and :math:`\beta=1/k_B T`.

.. _pull:

The pull code
-------------

:ref:`pull` The pull code applies forces or constraints between the
centers of mass of one or more pairs of groups of atoms. Each pull
reaction coordinate is called a “coordinate” and it operates on usually
two, but sometimes more, pull groups. A pull group can be part of one or
more pull coordinates. Furthermore, a coordinate can also operate on a
single group and an absolute reference position in space. The distance
between a pair of groups can be determined in 1, 2 or 3 dimensions, or
can be along a user-defined vector. The reference distance can be
constant or can change linearly with time. Normally all atoms are
weighted by their mass, but an additional weighting factor can also be
used.

.. _fig-pull:

.. figure:: plots/pull.*
   :width: 6.00000cm

   Schematic picture of pulling a lipid out of a lipid bilayer with
   umbrella pulling. :math:`V_{rup}` is the velocity at which the spring
   is retracted, :math:`Z_{link}` is the atom to which the spring is
   attached and :math:`Z_{spring}` is the location of the spring.

Several different pull types, i.e. ways to apply the pull force, are
supported, and in all cases the reference distance can be constant or
linearly changing with time.

#. **Umbrella pulling** A harmonic potential is applied between the
   centers of mass of two groups. Thus, the force is proportional to the
   displacement.

#. **Constraint pulling** The distance between the centers of mass of
   two groups is constrained. The constraint force can be written to a
   file. This method uses the SHAKE algorithm but only needs 1 iteration
   to be exact if only two groups are constrained.

#. **Constant force pulling** A constant force is applied between the
   centers of mass of two groups. Thus, the potential is linear. In this
   case there is no reference distance of pull rate.

#. **Flat bottom pulling** Like umbrella pulling, but the potential and
   force are zero for coordinate values below
   (``pull-coord?-type = flat-bottom``) or above
   (``pull-coord?-type = flat-bottom-high``) a reference
   value. This is useful for restraining e.g. the distance between two
   molecules to a certain region.

In addition, there are different types of reaction coordinates,
so-called pull geometries. These are set with the :ref:`mdp`
option ``pull-coord?-geometry``.

Definition of the center of mass
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

In |Gromacs|, there are three ways to define the center of mass of a
group. The standard way is a “plain” center of mass, possibly with
additional weighting factors. With periodic boundary conditions it is no
longer possible to uniquely define the center of mass of a group of
atoms. Therefore, a reference atom is used. For determining the center
of mass, for all other atoms in the group, the closest periodic image to
the reference atom is used. This uniquely defines the center of mass. By
default, the middle (determined by the order in the topology) atom is
used as a reference atom, but the user can also select any other atom if
it would be closer to center of the group.

For a layered system, for instance a lipid bilayer, it may be of
interest to calculate the PMF of a lipid as function of its distance
from the whole bilayer. The whole bilayer can be taken as reference
group in that case, but it might also be of interest to define the
reaction coordinate for the PMF more locally. The :ref:`mdp`
option ``pull-coord?-geometry = cylinder`` does not use all
the atoms of the reference group, but instead dynamically only those
within a cylinder with radius ``pull-cylinder-r`` around the
pull vector going through the pull group. This only works for distances
defined in one dimension, and the cylinder is oriented with its long
axis along this one dimension. To avoid jumps in the pull force,
contributions of atoms are weighted as a function of distance (in
addition to the mass weighting):

.. math::

   \begin{aligned}
   w(r < r_\mathrm{cyl}) & = &
   1-2 \left(\frac{r}{r_\mathrm{cyl}}\right)^2 + \left(\frac{r}{r_\mathrm{cyl}}\right)^4 \\
   w(r \geq r_\mathrm{cyl}) & = & 0\end{aligned}

Note that the radial dependence on the weight causes a radial force on
both cylinder group and the other pull group. This is an undesirable,
but unavoidable effect. To minimize this effect, the cylinder radius
should be chosen sufficiently large. The effective mass is 0.47 times
that of a cylinder with uniform weights and equal to the mass of uniform
cylinder of 0.79 times the radius.

.. _fig-pullref:

.. figure:: plots/pullref.*
   :width: 6.00000cm

   Comparison of a plain center of mass reference group versus a
   cylinder reference group applied to interface systems. C is the
   reference group. The circles represent the center of mass of two
   groups plus the reference group, :math:`d_c` is the reference
   distance.

For a group of molecules in a periodic system, a plain reference group
might not be well-defined. An example is a water slab that is connected
periodically in :math:`x` and :math:`y`, but has two liquid-vapor
interfaces along :math:`z`. In such a setup, water molecules can
evaporate from the liquid and they will move through the vapor, through
the periodic boundary, to the other interface. Such a system is
inherently periodic and there is no proper way of defining a “plain”
center of mass along :math:`z`. A proper solution is to using a cosine
shaped weighting profile for all atoms in the reference group. The
profile is a cosine with a single period in the unit cell. Its phase is
optimized to give the maximum sum of weights, including mass weighting.
This provides a unique and continuous reference position that is nearly
identical to the plain center of mass position in case all atoms are all
within a half of the unit-cell length. See ref :ref:`136 <refEngin2010a>`
for details.

When relative weights :math:`w_i` are used during the calculations,
either by supplying weights in the input or due to cylinder geometry or
due to cosine weighting, the weights need to be scaled to conserve
momentum:

.. math::

   w'_i = w_i
   \left. \sum_{j=1}^N w_j \, m_j \right/ \sum_{j=1}^N w_j^2 \, m_j

where :math:`m_j` is the mass of atom :math:`j` of the group. The mass
of the group, required for calculating the constraint force, is:

.. math:: M = \sum_{i=1}^N w'_i \, m_i

The definition of the weighted center of mass is:

.. math:: \mathbf{r}_{com} = \left. \sum_{i=1}^N w'_i \, m_i \, \mathbf{r}_i \right/ M

From the centers of mass the AFM, constraint, or umbrella force
:math:`\mathbf{F}_{\!com}` on each group can be
calculated. The force on the center of mass of a group is redistributed
to the atoms as follows:

.. math:: \mathbf{F}_{\!i} = \frac{w'_i \, m_i}{M} \, \mathbf{F}_{\!com}

Definition of the pull direction
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

The most common setup is to pull along the direction of the vector
containing the two pull groups, this is selected with
``pull-coord?-geometry = distance``. You might want to pull
along a certain vector instead, which is selected with
``pull-coord?-geometry = direction``. But this can cause
unwanted torque forces in the system, unless you pull against a
reference group with (nearly) fixed orientation, e.g. a membrane protein
embedded in a membrane along x/y while pulling along z. If your
reference group does not have a fixed orientation, you should probably
use ``pull-coord?-geometry = direction-relative``, see
:numref:`Fig. %s <fig-pulldirrel>`. Since the potential now depends
on the coordinates of two additional groups defining the orientation,
the torque forces will work on these two groups.

.. _fig-pulldirrel:

.. figure:: plots/pulldirrel.*
   :width: 5.00000cm

   The pull setup for geometry ``direction-relative``. The
   “normal” pull groups are 1 and 2. Groups 3 and 4 define the pull
   direction and thus the direction of the normal pull forces (red).
   This leads to reaction forces (blue) on groups 3 and 4, which are
   perpendicular to the pull direction. Their magnitude is given by the
   “normal” pull force times the ratio of :math:`d_p` and the distance
   between groups 3 and 4.

Definition of the angle and dihedral pull geometries
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Four pull groups are required for ``pull-coord?-geometry =
angle``. In the same way as for geometries with two groups, each
consecutive pair of groups :math:`i` and :math:`i+1` define a vector
connecting the COMs of groups :math:`i` and :math:`i+1`. The angle is
defined as the angle between the two resulting vectors. E.g., the
:ref:`mdp` option ``pull-coord?-groups = 1 2 2 4``
defines the angle between the vector from the COM of group 1 to the COM
of group 2 and the vector from the COM of group 2 to the COM of group 4.
The angle takes values in the closed interval [0, 180] deg. For
``pull-coord?-geometry = angle-axis`` the angle is defined
with respect to a reference axis given by
``pull-coord?-vec`` and only two groups need to be given.
The dihedral geometry requires six pull groups. These pair up in the
same way as described above and so define three vectors. The dihedral
angle is defined as the angle between the two planes spanned by the two
first and the two last vectors. Equivalently, the dihedral angle can be
seen as the angle between the first and the third vector when these
vectors are projected onto a plane normal to the second vector (the axis
vector). As an example, consider a dihedral angle involving four groups:
1, 5, 8 and 9. Here, the :ref:`mdp` option
``pull-coord?-groups = 8 1 1 5 5 9`` specifies the three
vectors that define the dihedral angle: the first vector is the COM
distance vector from group 8 to 1, the second vector is the COM distance
vector from group 1 to 5, and the third vector is the COM distance
vector from group 5 to 9. The dihedral angle takes values in the
interval (-180, 180] deg and has periodic boundaries.

Limitations
^^^^^^^^^^^

There is one theoretical limitation: strictly speaking, constraint
forces can only be calculated between groups that are not connected by
constraints to the rest of the system. If a group contains part of a
molecule of which the bond lengths are constrained, the pull constraint
and LINCS or SHAKE bond constraint algorithms should be iterated
simultaneously. This is not done in |Gromacs|. This means that for
simulations with ``constraints = all-bonds`` in the :ref:`mdp` file pulling is,
strictly speaking, limited to whole molecules or groups of molecules. In
some cases this limitation can be avoided by using the free energy code,
see sec. :ref:`fepmf`. In practice, the errors caused by not iterating
the two constraint algorithms can be negligible when the pull group
consists of a large amount of atoms and/or the pull force is small. In
such cases, the constraint correction displacement of the pull group is
small compared to the bond lengths.