be ignored (and if present in the :ref:`mdp` file, they unfortunately
generate warnings)
- .. mdp-value:: umbrella
-
- Center of mass pulling using an umbrella potential between the
- reference group and one or more groups.
-
- .. mdp-value:: constraint
-
- Center of mass pulling using a constraint between the reference
- group and one or more groups. The setup is identical to the
- option umbrella, except for the fact that a rigid constraint is
- applied instead of a harmonic potential.
-
- .. mdp-value:: constant-force
+ .. mdp-value:: yes
- Center of mass pulling using a linear potential and therefore a
- constant force. For this option there is no reference position
- and therefore the parameters :mdp:`pull-coord1-init` and
- :mdp:`pull-coord1-rate` are not used.
+ Center of mass pulling will be applied on 1 or more groups using
+ 1 or more pull coordinates.
-.. mdp:: pull-geometry
+.. mdp:: pull-cylinder-r
- .. mdp-value:: distance
+ (1.5) \[nm\]
+ the radius of the cylinder for
+ :mdp:`pull-coord1-geometry` = :mdp-value:`cylinder`
- Pull along the vector connecting the two groups. Components can
- be selected with :mdp:`pull-dim`.
-
- .. mdp-value:: direction
-
- Pull in the direction of :mdp:`pull-coord1-vec`.
+.. mdp:: pull-constr-tol
- .. mdp-value:: direction-periodic
+ (1e-6)
+ the relative constraint tolerance for constraint pulling
- As :mdp-value:`pull-geometry=direction`, but allows the distance
- to be larger than half the box size. With this geometry the box
- should not be dynamic (*e.g.* no pressure scaling) in the pull
- dimensions and the pull force is not added to virial.
+.. mdp:: pull-print-com1
- .. mdp-value:: cylinder
+ .. mdp-value:: no
- Designed for pulling with respect to a layer where the reference
- COM is given by a local cylindrical part of the reference
- group. The pulling is in the direction of
- :mdp:`pull-coord1-vec`. From the reference group a cylinder is
- selected around the axis going through the pull group with
- direction :mdp:`pull-coord1-vec` using two radii. The radius
- :mdp:`pull-r1` gives the radius within which all the relative
- weights are one, between :mdp:`pull-r1` and :mdp:`pull-r0` the
- weights are switched to zero. Mass weighting is also used. Note
- that the radii should be smaller than half the box size. For
- tilted cylinders they should be even smaller than half the box
- size since the distance of an atom in the reference group from
- the COM of the pull group has both a radial and an axial
- component.
-
-.. mdp:: pull-dim
+ do not print the COM of the first group in each pull coordinate
- (Y Y Y)
- the distance components to be used with :mdp:`pull-geometry`
- distance, and also sets which components are printed to the output
- files
+ .. mdp-value:: yes
-.. mdp:: pull-r1
+ print the COM of the first group in each pull coordinate
- (1) \[nm\]
- the inner radius of the cylinder for :mdp:`pull-geometry` cylinder
+.. mdp:: pull-print-com2
-.. mdp:: pull-r0
+ .. mdp-value:: no
- (1) \[nm\]
- the outer radius of the cylinder for :mdp:`pull-geometry` cylinder
+ do not print the COM of the second group in each pull coordinate
-.. mdp:: pull-constr-tol
+ .. mdp-value:: yes
- (1e-6)
- the relative constraint tolerance for constraint pulling
+ print the COM of the second group in each pull coordinate
-.. mdp:: pull-start
+.. mdp:: pull-print-ref-value
.. mdp-value:: no
- do not modify :mdp:`pull-coord1-init`
+ do not print the reference value for each pull coordinate
.. mdp-value:: yes
- add the COM distance of the starting conformation to
- :mdp:`pull-coord1-init`
+ print the reference value for each pull coordinate
-.. mdp:: pull-print-reference
+.. mdp:: pull-print-components
.. mdp-value:: no
- do not print the COM of the first group in each pull coordinate
-
+ only print the distance for each pull coordinate
+
.. mdp-value:: yes
- print the COM of the first group in each pull coordinate
+ print the distance and Cartesian components selected in
+ :mdp:`pull-coord1-dim`
.. mdp:: pull-nstxout
- (10)
- frequency for writing out the COMs of all the pull group
+ (50)
+ frequency for writing out the COMs of all the pull group (0 is
+ never)
.. mdp:: pull-nstfout
- (1)
+ (50)
frequency for writing out the force of all the pulled group
+ (0 is never)
+
.. mdp:: pull-ngroups
and one should think about what to do with the center of mass
motion.
+.. mdp:: pull-coord1-type:
+
+ .. mdp-value:: umbrella
+
+ Center of mass pulling using an umbrella potential between the
+ reference group and one or more groups.
+
+ .. mdp-value:: constraint
+
+ Center of mass pulling using a constraint between the reference
+ group and one or more groups. The setup is identical to the
+ option umbrella, except for the fact that a rigid constraint is
+ applied instead of a harmonic potential.
+
+ .. mdp-value:: constant-force
+
+ Center of mass pulling using a linear potential and therefore a
+ constant force. For this option there is no reference position
+ and therefore the parameters :mdp:`pull-coord1-init` and
+ :mdp:`pull-coord1-rate` are not used.
+
+ .. mdp-value:: flat-bottom
+
+ At distances beyond :mdp:`pull-coord1-init` a harmonic potential
+ is applied, otherwise no potential is applied.
+
+.. mdp:: pull-coord1-geometry
+
+ .. mdp-value:: distance
+
+ Pull along the vector connecting the two groups. Components can
+ be selected with :mdp:`pull-coord1-dim`.
+
+ .. mdp-value:: direction
+
+ Pull in the direction of :mdp:`pull-coord1-vec`.
+
+ .. mdp-value:: direction-periodic
+
+ As :mdp-value:`direction`, but allows the distance to be larger
+ than half the box size. With this geometry the box should not be
+ dynamic (*e.g.* no pressure scaling) in the pull dimensions and
+ the pull force is not added to virial.
+
+ .. mdp-value:: cylinder
+
+ Designed for pulling with respect to a layer where the reference
+ COM is given by a local cylindrical part of the reference group.
+ The pulling is in the direction of :mdp:`pull-coord1-vec`. From
+ the first of the two groups in :mdp:`pull-coord1-groups` a
+ cylinder is selected around the axis going through the COM of
+ the second group with direction :mdp:`pull-coord1-vec` with
+ radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
+ continously to zero as the radial distance goes from 0 to
+ :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
+ dependence gives rise to radial forces on both pull groups.
+ Note that the radius should be smaller than half the box size.
+ For tilted cylinders they should be even smaller than half the
+ box size since the distance of an atom in the reference group
+ from the COM of the pull group has both a radial and an axial
+ component. This geometry is not supported with constraint
+ pulling.
+
+.. mdp:: pull-coord1-dim
+
+ (Y Y Y)
+ Selects the dimensions that this pull coordinate acts on and that
+ are printed to the output files when
+ :mdp:`pull-print-components` = :mdp-value:`yes`. With
+ :mdp:`pull-coord1-geometry` = :mdp-value:`distance`, only Cartesian
+ components set to Y contribute to the distance. Thus setting this
+ to Y Y N results in a distance in the x/y plane. With other
+ geometries all dimensions with non-zero entries in
+ :mdp:`pull-coord1-vec` should be set to Y, the values for other
+ dimensions only affect the output.
+
.. mdp:: pull-coord1-origin
(0.0 0.0 0.0)
(0.0 0.0 0.0)
The pull direction. :ref:`gmx grompp` normalizes the vector.
+.. mdp:: pull-coord1-start
+
+ .. mdp-value:: no
+
+ do not modify :mdp:`pull-coord1-init`
+
+ .. mdp-value:: yes
+
+ add the COM distance of the starting conformation to
+ :mdp:`pull-coord1-init`
+
.. mdp:: pull-coord1-init
(0.0) \[nm\]
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff