distance restraints over an ensemble of molecules in one
simulation box. Normally, one would perform ensemble averaging
- over multiple subsystems, each in a separate box, using ``mdrun
- -multi``. Supply ``topol0.tpr``, ``topol1.tpr``, ... with
- different coordinates and/or velocities. The environment
+ over multiple simulations, using ``mdrun
+ -multidir``. The environment
variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
- within each ensemble (usually equal to the ``mdrun -multi``
- value).
+ within each ensemble (usually equal to the number of directories
+ supplied to ``mdrun -multidir``).
.. mdp:: disre-weighting
.. mdp-value:: yes
use orientation restraints, ensemble averaging can be performed
- with `mdrun -multi`
+ with ``mdrun -multidir``
.. mdp:: orire-fc
CASSCF method.
-Implicit solvent
-^^^^^^^^^^^^^^^^
-
-.. mdp:: implicit-solvent
-
- .. mdp-value:: no
-
- No implicit solvent
-
- .. mdp-value:: GBSA
-
- Do a simulation with implicit solvent using the Generalized Born
- formalism. Three different methods for calculating the Born
- radii are available, Still, HCT and OBC. These are specified
- with the :mdp:`gb-algorithm` field. The non-polar solvation is
- specified with the :mdp:`sa-algorithm` field.
-
-.. mdp:: gb-algorithm
-
- .. mdp-value:: Still
-
- Use the Still method to calculate the Born radii
-
- .. mdp-value:: HCT
-
- Use the Hawkins-Cramer-Truhlar method to calculate the Born
- radii
-
- .. mdp-value:: OBC
-
- Use the Onufriev-Bashford-Case method to calculate the Born
- radii
-
-.. mdp:: nstgbradii
-
- (1) \[steps\]
- Frequency to (re)-calculate the Born radii. For most practial
- purposes, setting a value larger than 1 violates energy
- conservation and leads to unstable trajectories.
-
-.. mdp:: rgbradii
-
- (1.0) \[nm\]
- Cut-off for the calculation of the Born radii. Currently must be
- equal to rlist
-
-.. mdp:: gb-epsilon-solvent
-
- (80)
- Dielectric constant for the implicit solvent
-
-.. mdp:: gb-saltconc
-
- (0) \[M\]
- Salt concentration for implicit solvent models, currently not used
-
-.. mdp:: gb-obc-alpha
-.. mdp:: gb-obc-beta
-.. mdp:: gb-obc-gamma
-
- Scale factors for the OBC model. Default values of 1, 0.78 and 4.85
- respectively are for OBC(II). Values for OBC(I) are 0.8, 0 and 2.91
- respectively
-
-.. mdp:: gb-dielectric-offset
-
- (0.009) \[nm\]
- Distance for the di-electric offset when calculating the Born
- radii. This is the offset between the center of each atom the
- center of the polarization energy for the corresponding atom
-
-.. mdp:: sa-algorithm
-
- .. mdp-value:: Ace-approximation
-
- Use an Ace-type approximation
-
- .. mdp-value:: None
-
- No non-polar solvation calculation done. For GBSA only the polar
- part gets calculated
-
-.. mdp:: sa-surface-tension
-
- \[kJ mol-1 nm-2\]
- Default value for surface tension with SA algorithms. The default
- value is -1; Note that if this default value is not changed it will
- be overridden by :ref:`gmx grompp` using values that are specific
- for the choice of radii algorithm (0.0049 kcal/mol/Angstrom^2 for
- Still, 0.0054 kcal/mol/Angstrom2 for HCT/OBC) Setting it to 0 will
- while using an sa-algorithm other than None means no non-polar
- calculations are done.
-
-
Computational Electrophysiology
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Use these options to switch on and control ion/water position exchanges in "Computational
Removed features
^^^^^^^^^^^^^^^^
-This feature has been removed from |Gromacs|, but so that old
+These features have been removed from |Gromacs|, but so that old
:ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
fatal error if this is set.
(no)
+.. mdp:: implicit-solvent
+
+ (no)
+
.. _reference manual: gmx-manual-parent-dir_
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff