| ## mdp options Main Table of Contents | VERSION 3.2 Sun 25 Jan 2004

### Table of Contents

- General remarks

- preprocessing (title, warnings, cpp, include, define)
- run control (integrator, tinit, dt, nsteps, init_step, comm_mode, nstcomm, comm_grps)
- langevin dynamics (bd_temp, bd_fric, ld_seed)
- energy minimization (emtol, emstep, nstcgsteep)
- shell molecular dynamics(emtol,niter)
- output control (nstxout, nstvout, nstfout, nstlog, nstenergy, nstxtcout, xtc_precision, xtc_grps, energygrps)
- neighbor searching (nstlist, ns_type, pbc, rlist)
- electrostatics and VdW (coulombtype, rcoulomb_switch, rcoulomb, vdwtype, rvdw_switch, rvdw, epsilon_r, DispCorr, fourierspacing, fourier_nx, fourier_ny, fourier_nz, pme_order, ewald_rtol, ewald_geometry, surface_epsilon, optimize_fft)
- Temperature coupling (tcoupl, tc_grps, tau_t, ref_t)
- Pressure coupling (pcoupl, pcoupltype, tau_p, compressibility, ref_p)
- simulated annealing (annealing, annealing_npoints, annealing_time, annealing_temp)
- velocity generation (gen_vel, gen_temp, gen_seed)
- bonds (constraints, constraint_algorithm, unconstrained_start, shake_tol, lincs_order, lincs_iter, lincs_warnangle, morse)
- Energy group exclusions (energygrp_excl)
- NMR refinement (disre, disre_weighting, disre_mixed, disre_fc, disre_tau, nstdisreout, orire, orire_fc, orire_tau, orire_fitgrp, nstorireout)
- Free Energy Perturbation (free_energy, init_lambda, delta_lambda, sc_alpha, sc_sigma)
- Non-equilibrium MD (acc_grps, accelerate, freezegrps, freezedim, cos_acceleration)
- Electric fields (E_x, E_xt, E_y, E_yt, E_z, E_zt )
- User defined thingies (user1_grps, user2_grps, userint1, userint2, userint3, userint4, userreal1, userreal2, userreal3, userreal4)
- Index

### General

Default values are given in parentheses. The first option is always the default option. Units are given in square brackets The difference between a dash and an underscore is ignored.

A sample `.mdp` file is available. This should be appropriate to start a normal simulation. Edit it to suit your specific needs and desires.

### Preprocessing

#### title:

  this is redundant, so you can type anything you want

#### cpp: (/lib/cpp)

  your preprocessor

#### include:

  directories to include in your topology. Format:

      -I/home/john/my_lib -I../more_lib

#### define: ()

  defines to pass to the preprocessor, default is no defines. You can use any defines to control options in your customized topology files. Options that are already available by default are:
  -DFLEX_SPC
    Will tell grompp to include FLEX_SPC in stead of SPC into your topology, this is necessary to make conjugate gradients or l-bfgs minimization work and will allow steepest descent to minimize further.
  -DPOSRE
    Will tell grompp to include posre.itp into your topology, used for position restraints.

### Run control

#### integrator:

md
  A leap-frog algorithm for integrating Newton's equations of motion.
sd
  A leap-frog stochastic dynamics integrator. The temperature for one or more groups of atoms (tc_grps) is set with ref_t [K], the inverse friction constant for each group is set with tau_t [ps]. The parameter tcoupl is ignored. The random generator is initialized with ld_seed.
  NOTE: temperature deviations decay twice as fast as with a Berendsen thermostat with the same tau_t.
bd
  An Euler integrator for Brownian or position Langevin dynamics, the velocity is the force divided by a friction coefficient (bd_fric [amu ps-1]) plus random thermal noise (bd_temp [K]). When bd_fric=0, the friction coefficient for each particle is calculated as mass/tau_t, as for the integrator `sd`. The random generator is initialized with ld_seed.
The following algorithms are not integrators, but selected using the integrator tag anyway
steep
  A steepest descent algorithm for energy minimization. The maximum step size is emstep [nm], the tolerance is emtol [kJ mol-1 nm-1].
cg
  A conjugate gradient algorithm for energy minimization, the tolerance is emtol [kJ mol-1 nm-1]. CG is more efficient when a steepest descent step is done every once in a while, this is determined by nstcgsteep. For a minimization prior to a normal mode analysis, which requires a very high accuracy, GROMACS should be compiled in double precision.
l-bfgs
  A quasi-Newtonian algorithm for energy minimization according to the low-memory Broyden-Fletcher-Goldfarb-Shanno approach. In practice this seems to converge faster than Conjugate Gradients, but due to the correction steps necessary it is not (yet) parallelized.
nm
  Normal mode analysis is performed on the structure in the `tpr` file
. GROMACS should be compiled in double precision.

#### tinit: (0) [ps]

  starting time for your run (only makes sense for integrators `md`, `sd` and `bd`)

#### dt: (0.001) [ps]

  time step for integration (only makes sense for integrators `md`, `sd` and `bd`)

#### nsteps: (0)

  maximum number of steps to integrate

#### init_step: (0)

  The starting step. The time at an step i in a run is calculated as: t = `tinit` + `dt`*(`init_step` + i). The free-energy lambda is calculated as: lambda = `init_lambda` + `delta_lambda`*(`init_step` + i). Also non-equilibrium MD parameters can depend on the step number. Thus for exact restarts or redoing part of a run it might be necessary to set `init_step` to the step number of the restart frame. `tpbconv` does this automatically.

#### comm_mode:

  Linear
    Remove center of mass translation
  Angular
    Remove center of mass translation and rotation around the center of mass
  No
    No restriction on the center of mass motion

#### nstcomm: (1) [steps]

  frequency for center of mass motion removal

#### comm_grps:

  group(s) for center of mass motion removal, default is the whole system

### Langevin dynamics

#### bd_temp: (300) [K]

  temperature in Brownian dynamics run (controls thermal noise level). When bd_fric=0, ref_t is used instead.

#### bd_fric: (0) [amu ps-1]

  Brownian dynamics friction coefficient. When bd_fric=0, the friction coefficient for each particle is calculated as mass/tau_t.

#### ld_seed: (1993) [integer]

  used to initialize random generator for thermal noise for stochastic and Brownian dynamics. When ld_seed is set to -1, the seed is calculated as `(time() + getpid()) % 1000000`
. When running on multiple processors, each processor uses a seed equal to ld_seed plus the processor number.

### Energy minimization

#### emtol: (100.0) [kJ mol-1 nm-1]

  the minimization is converged when the maximum force is smaller than this value

#### emstep: (0.01) [nm]

  initial step-size

#### nstcgsteep: (1000) [steps]

  frequency of performing 1 steepest descent step while doing conjugate gradient energy minimization.

#### nbfgscorr: (10)

  Number of correction steps to use for L-BFGS minimization. A higher number is (at least theoretically) more accurate, but slower.

### Shell Molecular Dynamics

When doing shell molecular dynamics the positions of the shells are optimized at every time step until either the RMS force on the shells is less than emtol, or a maximum number of iterations (niter) has been reached

#### emtol: (100.0) [kJ mol-1 nm-1]

  the minimization is converged when the maximum force is smaller than this value. For shell MD this value should be 1.0 at most, but since the variable is used for energy minimization as well the default is 100.0.

#### niter: (20)

  maximum number of iterations for optimizing the shell positions.

### Output control

#### nstxout: (100) [steps]

  frequency to write coordinates to output trajectory file, the last coordinates are always written

#### nstvout: (100) [steps]

  frequency to write velocities to output trajectory, the last velocities are always written

#### nstfout: (0) [steps]

  frequency to write forces to output trajectory.

#### nstlog: (100) [steps]

  frequency to write energies to log file, the last energies are always written

#### nstenergy: (100) [steps]

  frequency to write energies to energy file, the last energies are always written

#### nstxtcout: (0) [steps]

  frequency to write coordinates to xtc trajectory

#### xtc_precision: (1000) [real]

  precision to write to xtc trajectory

#### xtc_grps:

  group(s) to write to xtc trajectory, default the whole system is written (if nstxtcout is larger than zero)

#### energygrps:

  group(s) to write to energy file

### Neighbor searching

#### nstlist: (10) [steps]

  Frequency to update the neighbor list (and the long-range forces, when using twin-range cut-off's). When this is 0, the neighbor list is made only once.

#### ns_type:

  grid
    Make a grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list every nstlist steps. In large systems grid search is much faster than simple search.
  simple
    Check every atom in the box when constructing a new neighbor list every nstlist steps.

#### pbc:

  xyz
    Use periodic boundary conditions in all directions.
  no
    Use no periodic boundary conditions, ignore the box. To simulate without cut-offs, set all cut-offs to 0 and nstlist=0.

#### rlist: (1) [nm]

  cut-off distance for the short-range neighbor list

### Electrostatics and VdW

#### coulombtype:

  Cut-off
    Twin range cut-off's with neighborlist cut-off rlist and Coulomb cut-off rcoulomb, where rcoulomb >= rlist. The dielectric constant is set with epsilon_r.
  Ewald
    Classical Ewald sum electrostatics. Use e.g. rlist=0.9, rcoulomb=0.9. The highest magnitude of wave vectors used in reciprocal space is controlled by fourierspacing. The relative accuracy of direct/reciprocal space is controlled by ewald_rtol.
    NOTE: Ewald scales as O(N3/2) and is thus extremely slow for large systems. It is included mainly for reference - in most cases PME will perform much better.
  PME
    Fast Particle-Mesh Ewald electrostatics. Direct space is similar to the Ewald sum, while the reciprocal part is performed with FFTs. Grid dimensions are controlled with fourierspacing and the interpolation order with pme_order. With a grid spacing of 0.1 nm and cubic interpolation the electrostatic forces have an accuracy of 2-3e-4. Since the error from the vdw-cutoff is larger than this you might try 0.15 nm. When running in parallel the interpolation parallelizes better than the FFT, so try decreasing grid dimensions while increasing interpolation.
  PPPM
    Particle-Particle Particle-Mesh algorithm for long range electrostatic interactions. Use for example rlist`=0.9`, rcoulomb`=0.9`. The grid dimensions are controlled by fourierspacing. Reasonable grid spacing for PPPM is 0.05-0.1 nm. See `Shift` for the details of the particle-particle potential.
    NOTE: the pressure in incorrect when using PPPM.
  Reaction-Field
    Reaction field with Coulomb cut-off rcoulomb, where rcoulomb >= rlist. The dielectric constant beyond the cut-off is epsilon_r. The dielectric constant can be set to infinity by setting epsilon_r=0.
  Generalized-Reaction-Field
    Generalized reaction field with Coulomb cut-off rcoulomb, where rcoulomb >= rlist. The dielectric constant beyond the cut-off is epsilon_r. The ionic strength is computed from the number of charged (i.e. with non zero charge) charge groups. The temperature for the GRF potential is set with ref_t [K].
  Shift
    The Coulomb potential is decreased over the whole range and the forces decay smoothly to zero between rcoulomb_switch and rcoulomb. The neighbor search cut-off rlist should be 0.1 to 0.3 nm larger than rcoulomb to accommodate for the size of charge groups and diffusion between neighbor list updates.
  Switch
    The Coulomb potential is normal out to rcoulomb_switch, after which it is switched off to reach zero at rcoulomb. Both the potential and force functions are continuously smooth, but be aware that all switch functions will give rise to a bulge (increase) in the force (since we are switching the potential). The neighbor search cut-off rlist should be 0.1 to 0.3 nm larger than rcoulomb to accommodate for the size of charge groups and diffusion between neighbor list updates.
  User
    `mdrun` will now expect to find a file `table.xvg` with user-defined potential functions for repulsion, dispersion and Coulomb. This file should contain 7 columns: the `x` value, `f(x)`, `-f(2)(x)`, `g(x)`, `-g(2)(x)`, `h(x)`, `-h(2)(x)`, where `f(2)(x)` denotes the `2nd` derivative of function `f(x)` with respect to `x`. f(x) is the Coulomb function, g(x) the dispersion function and h(x) the repulsion function. The `x` values should run from 0 to the largest cut-off distance + table-extension and should be uniformly spaced. The optimal spacing, which is used for non-user tables, is `0.002` [nm] when you run in single precision or `0.0005` [nm] when you run in double precision. The function value at `x=0` is not important. More information is in the printed manual.

#### rcoulomb_switch: (0) [nm]

  where to start switching the Coulomb potential

#### rcoulomb: (1) [nm]

  distance for the Coulomb cut-off

#### epsilon_r: (1)

  dielectric constant

#### vdwtype:

  Cut-off
    Twin range cut-off's with neighbor list cut-off rlist and VdW cut-off rvdw, where rvdw `>=` rlist.
  Shift
    The LJ (not Buckingham) potential is decreased over the whole range and the forces decay smoothly to zero between rvdw_switch and rvdw. The neighbor search cut-off rlist should be 0.1 to 0.3 nm larger than rvdw to accommodate for the size of charge groups and diffusion between neighbor list updates.
  Switch
    The LJ (not Buckingham) potential is normal out to rvdw_switch, after which it is switched off to reach zero at rvdw. Both the potential and force functions are continuously smooth, but be aware that all switch functions will give rise to a bulge (increase) in the force (since we are switching the potential). The neighbor search cut-off rlist should be 0.1 to 0.3 nm larger than rvdw to accommodate for the size of charge groups and diffusion between neighbor list updates.
  User
    See above The function value at `x=0` is not important. When you want to use LJ correction, make sure that rvdw corresponds to the cut-off in the user-defined function.

#### rvdw_switch: (0) [nm]

  where to start switching the LJ potential

#### rvdw: (1) [nm]

  distance for the LJ or Buckingham cut-off

#### DispCorr:

no
  don't apply any correction
EnerPres
  apply long range dispersion corrections for Energy and Pressure
Ener
  apply long range dispersion corrections for Energy only

#### table-extension: (1) [nm]

  Extension of the non-bonded potential lookup tables beyond the largest cut-off distance. The value should be large enough to account for charge group sizes and the diffusion between neighbor-list updates. This value also specifies the length of the lookup tables for the 1-4 interactions, which are always tabulated irrespective of the use of tables for the non-bonded interactions.

#### fourierspacing: (0.12) [nm]

  The maximum grid spacing for the FFT grid when using PPPM or PME. For ordinary Ewald the spacing times the box dimensions determines the highest magnitude to use in each direction. In all cases each direction can be overridden by entering a non-zero value for fourier_n*.

#### fourier_nx (0) ; fourier_ny (0) ; fourier_nz: (0)

  Highest magnitude of wave vectors in reciprocal space when using Ewald.
  Grid size when using PPPM or PME. These values override fourierspacing per direction. The best choice is powers of 2, 3, 5 and 7. Avoid large primes.

#### pme_order (4)

  Interpolation order for PME. 4 equals cubic interpolation. You might try 6/8/10 when running in parallel and simultaneously decrease grid dimension.

#### ewald_rtol (1e-5)

  The relative strength of the Ewald-shifted direct potential at the cutoff is given by ewald_rtol. Decreasing this will give a more accurate direct sum, but then you need more wave vectors for the reciprocal sum.

#### ewald_geometry: (3d)

  The geometry to use for Ewald summations. 3d means the sum is performed in all three dimensions. If your system has a slab geometry in the x-y plane you can try to increase box z dimension and use the 3dc geometry. The reciprocal sum is still performed in 3d, but a force and potential correction applied in the z dimension to produce a pseudo-2d summation. In the future there might also be a true 2d option, but this is not working yet.

#### surface_epsilon: (0)

  This controls the dipole correction to the Ewald summation in 3d. The default value of zero means it is turned off. Turn it on by setting it to the value of the relative permittivity of the imaginary surface around your infinite system. Be careful - you shouldn't use this if you have free mobile charges in your system. This value does not affect the slab 3DC variant of the long range corrections.

#### optimize_fft:

  no
    Don't calculate the optimal FFT plan for the grid at startup.
  yes
    Calculate the optimal FFT plan for the grid at startup. This saves a few percent for long simulations, but takes a couple of minutes at start.

### Temperature coupling

#### tcoupl:

  no
    No temperature coupling.
  berendsen
    Temperature coupling with a Berendsen-thermostat to a bath with temperature ref_t [K], with time constant tau_t [ps]. Several groups can be coupled separately, these are specified in the tc_grps field separated by spaces.
  nose-hoover
    Temperature coupling with a by using a Nose-Hoover extended ensemble. The reference temperature and coupling groups are selected as above, but in this case tau_t [ps] controls the period of the temperature fluctuations at equilibrium, which is slightly different from a relaxation time.

#### tc_grps:

  groups to couple separately to temperature bath

#### tau_t: [ps]

  time constant for coupling (one for each group in tc_grps)

#### ref_t: [K]

  reference temperature for coupling (one for each group in tc_grps)

### Pressure coupling

#### pcoupl:

  no
    No pressure coupling. This means a fixed box size.
  berendsen
    Exponential relaxation pressure coupling with time constant tau_p [ps]. The box is scaled every timestep. It has been argued that this does not yield a correct thermodynamic ensemble, but it is the most efficient way to scale a box at the beginning of a run.
  Parrinello-Rahman
    Extended-ensemble pressure coupling where the box vectors are subject to an equation of motion. The equation of motion for the atoms is coupled to this. No instantaneous scaling takes place. As for Nose-Hoover temperature coupling the time constant tau_p [ps] is the period of pressure fluctuations at equilibrium. This is probably a better method when you want to apply pressure scaling during data collection, but beware that you can get very large oscillations if you are starting from a different pressure.

#### pcoupltype:

  isotropic
    Isotropic pressure coupling with time constant tau_p [ps]. The compressibility and reference pressure are set with compressibility [bar-1] and ref_p [bar], one value is needed.
  semiisotropic
    Pressure coupling which is isotropic in the x and y direction, but different in the z direction. This can be useful for membrane simulations. 2 values are needed for x/y and z directions respectively.
  anisotropic
    Idem, but 6 values are needed for xx, yy, zz, xy/yx, xz/zx and yz/zy components respectively. When the off-diagonal compressibilities are set to zero, a rectangular box will stay rectangular. Beware that anisotropic scaling can lead to extreme deformation of the simulation box.
  surface-tension
    Surface tension coupling for surfaces parallel to the xy-plane. Uses normal pressure coupling for the z-direction, while the surface tension is coupled to the x/y dimensions of the box. The first ref_p value is the reference surface tension times the number of surfaces [bar nm], the second value is the reference z-pressure [bar]. The two compressibility [bar-1] values are the compressibility in the x/y and z direction respectively. The value for the z-compressibility should be reasonably accurate since it influences the converge of the surface-tension, it can also be set to zero to have a box with constant height.
  triclinic
    Fully dynamic box - supported, but experimental. You should provide six values for the compressibility and reference pressure.

#### tau_p: (1) [ps]

  time constant for coupling

#### compressibility: [bar-1]

  compressibility (NOTE: this is now really in bar-1) For water at 1 atm and 300 K the compressibility is 4.5e-5 [bar-1].

#### ref_p: [bar]

  reference pressure for coupling

### Simulated annealing

Simulated annealing is controlled separately for each temperature group in Gromacs. The reference temperature is a piecewise linear function, but you can use an arbitrary number of points for each group, and choose either a single sequence or a periodic behaviour for each group. The actual annealing is performed by dynamically changing the reference temperature used in the thermostat algorithm selected, so remember that the system will usually not instantaneously reach the reference temperature!

#### annealing:

  Type of annealing for each temperature group
no
  No simulated annealing - just couple to reference temperature value.
single
  A single sequence of annealing points. If your simulation is longer than the time of the last point, the temperature will be coupled to this constant value after the annealing sequence has reached the last time point.
periodic
  The annealing will start over at the first reference point once the last reference time is reached. This is repeated until the simulation ends.

#### annealing_npoints:

  A list with the number of annealing reference/control points used for each temperature group. Use 0 for groups that are not annealed. The number of entries should equal the number of temperature groups.

#### annealing_time:

  List of times at the annealing reference/control points for each group. If you are using periodic annealing, the times will be used modulo the last value, i.e. if the values are 0, 5, 10, and 15, the coupling will restart at the 0ps value after 15ps, 30ps, 45ps, etc. The number of entries should equal the sum of the numbers given in annealing_npoints.

#### annealing_temp:

  List of temperatures at the annealing reference/control points for each group. The number of entries should equal the sum of the numbers given in annealing_npoints.
Confused? OK, let's use an example. Assume you have two temperature groups, set the group selections to `annealing = single periodic`, the number of points of each group to `annealing_npoints = 3 4`, the times to `annealing_time = 0 3 6 0 2 4 6` and finally temperatures to `annealing_temp = 298 280 270 298 320 320 298`. The first group will be coupled to 298K at 0ps, but the reference temperature will drop linearly to reach 280K at 3ps, and then linearly between 280K and 270K from 3ps to 6ps. After this is stays constant, at 270K. The second group is coupled to 298K at 0ps, it increases linearly to 320K at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it decreases to 298K, and then it starts over with the same pattern again, i.e. rising linearly from 298K to 320K between 6ps and 8ps. Check the summary printed by grompp if you are unsure!

### Velocity generation

#### gen_vel:

  no
    Do not generate velocities at startup. The velocities are set to zero when there are no velocities in the input structure file.
  yes
    Generate velocities according to a Maxwell distribution at temperature gen_temp [K], with random seed gen_seed. This is only meaningful with integrator md.

#### gen_temp: (300) [K]

  temperature for Maxwell distribution

#### gen_seed: (173529) [integer]

  used to initialize random generator for random velocities, when gen_seed is set to -1, the seed is calculated as `(time() + getpid()) % 1000000`

### Bonds

#### constraints:

  none
    No constraints, i.e. bonds are represented by a harmonic or a Morse potential (depending on the setting of morse) and angles by a harmonic potential.
  hbonds
    Only constrain the bonds with H-atoms.
  all-bonds
    Constrain all bonds.
  h-angles
    Constrain all bonds and constrain the angles that involve H-atoms by adding bond-constraints.
  all-angles
    Constrain all bonds and constrain all angles by adding bond-constraints.

#### constraint_algorithm:

  lincs
    LINear Constraint Solver. The accuracy in set with lincs_order, which sets the number of matrices in the expansion for the matrix inversion, 4 is enough for a "normal" MD simulation, 8 is needed for BD with large time-steps. After the matrix inversion correction the algorithm does an iterative correction to compensate for lengthening due to rotation. The number of such iterations can be controlled with lincs_iter. The accuracy of the constraints is printed to the log file every nstlog steps. If a bond rotates more than lincs_warnangle [degrees] in one step, a warning will be printed both to the log file and to `stderr`. Lincs should not be used with coupled angle constraints.
  shake
    Shake is slower and less stable than Lincs, but does work with angle constraints. The relative tolerance is set with shake_tol, 0.0001 is a good value for "normal" MD.

#### unconstrained_start:

  no
    apply constraints to the start configuration
  yes
    do not apply constraints to the start configuration

#### shake_tol: (0.0001)

  relative tolerance for shake

#### lincs_order: (4)

  Highest order in the expansion of the constraint coupling matrix.

#### lincs_iter: (1)

  Number of iterations to correct for rotational lengthening in Lincs. For normal runs a single step is sufficient, but for NVE runs where you want to conserve energy accurately you might want to increase it to 2, and for energy minimization with constraints it is sometimes necessary to use 4 or even 8 (double precision) iteration steps.

#### lincs_warnangle: (30) [degrees]

  maximum angle that a bond can rotate before Lincs will complain

#### morse:

  no
    bonds are represented by a harmonic potential
  yes
    bonds are represented by a Morse potential

### Energy group exclusions

#### energygrp_excl:

  Pairs of energy groups for which all non-bonded interactions are excluded. An example: if you have two energy groups `Protein` and `SOL`, specifying
  `energy_excl = Protein Protein SOL SOL`
  would give only the non-bonded interactions between the protein and the solvent. This is especially useful for speeding up energy calculations with `mdrun -rerun` and for excluding interactions within frozen groups.

### NMR refinement

#### disre:

  no
    no distance restraints (ignore distance restraint information in topology file)
  simple
    simple (per-molecule) distance restraints, ensemble averaging can be performed with `mdrun -multi`
  ensemble
    distance restraints over an ensemble of molecules in one simulation box, should only be used for special cases, such as dimers

#### disre_weighting:

  conservative
    the forces are the derivative of the restraint potential, this results in an r-7 weighting of the atom pairs
  equal
    divide the restraint force equally over all atom pairs in the restraint

#### disre_mixed:

  no
    the violation used in the calculation of the restraint force is the time averaged violation
  yes
    the violation used in the calculation of the restraint force is the square root of the time averaged violation times the instantaneous violation

#### disre_fc: (1000) [kJ mol-1 nm-2]

  force constant for distance restraints, which is multiplied by a (possibly) different factor for each restraint

#### disre_tau: (0) [ps]

  time constant for distance restraints running average

#### nstdisreout: (100) [steps]

  frequency to write the running time averaged and instantaneous distances of all atom pairs involved in restraints to the energy file (can make the energy file very large)

#### orire:

  no
    no orientation restraints (ignore orientation restraint information in topology file)
  yes
    use orientation restraints, ensemble averaging can be performed with `mdrun -multi`

#### orire_fc: (0) [kJ mol]

  force constant for orientation restraints, which is multiplied by a (possibly) different factor for each restraint, can be set to zero to obtain the orientations from a free simulation

#### orire_tau: (0) [ps]

  time constant for orientation restraints running average

#### orire_fitgrp:

  fit group for orientation restraining, for a protein backbone is a good choice

#### nstorireout: (100) [steps]

  frequency to write the running time averaged orientations for all restraints to the energy file (can make the energy file very large)

### Free Energy Perturbation

#### free_energy:

  no
    Only use topology A.
  yes
    Interpolate between topology A (lambda=0) to topology B (lambda=1) and write the derivative of the Hamiltonian with respect to lambda to the energy file and to `dgdl.xvg`. The potentials, bond-lengths and angles are interpolated linearly as described in the manual. When sc_alpha is larger than zero, soft-core potentials are used for the LJ and Coulomb interactions.

#### init_lambda: (0)

  starting value for lambda

#### delta_lambda: (0)

  increment per time step for lambda

#### sc_alpha: (0)

  the soft-core parameter, a value of 0 results in linear interpolation of the LJ and Coulomb interactions

#### sc_sigma: (0.3) [nm]

  the soft-core sigma for particles which have a C6 or C12 parameter equal to zero

### Non-equilibrium MD

#### acc_grps:

  groups for constant acceleration (e.g.: `Protein Sol`) all atoms in groups Protein and Sol will experience constant acceleration as specified in the accelerate line

#### accelerate: (0) [nm ps-2]

  acceleration for acc_grps; x, y and z for each group (e.g. `0.1 0.0 0.0 -0.1 0.0 0.0` means that first group has constant acceleration of 0.1 nm ps-2 in X direction, second group the opposite).

#### freezegrps:

  Groups that are to be frozen (i.e. their X, Y, and/or Z position will not be updated; e.g. `Lipid SOL`). freezedim specifies for which dimension the freezing applies. You might want to use energy group exclusions for completely frozen groups.

#### freezedim:

  dimensions for which groups in freezegrps should be frozen, specify `Y` or `N` for X, Y and Z and for each group (e.g. `Y Y N N N N` means that particles in the first group can move only in Z direction. The particles in the second group can move in any direction).

#### cos_acceleration: (0) [nm ps-2]

  the amplitude of the acceleration profile for calculating the viscosity. The acceleration is in the X-direction and the magnitude is cos_acceleration cos(2 pi z/boxheight). Two terms are added to the energy file: the amplitude of the velocity profile and 1/viscosity.

### Electric fields

#### E_x ; E_y ; E_z:

  If you want to use an electric field in a direction, enter 3 numbers after the appropriate E_*, the first number: the number of cosines, only 1 is implemented (with frequency 0) so enter 1, the second number: the strength of the electric field in V nm-1, the third number: the phase of the cosine, you can enter any number here since a cosine of frequency zero has no phase.

#### E_xt; E_yt; E_zt:

  not implemented yet

### User defined thingies

#### user1_grps; user2_grps:

#### userint1 (0); userint2 (0); userint3 (0); userint4 (0)

#### userreal1 (0); userreal2 (0); userreal3 (0); userreal4 (0)

  These you can use if you modify code. You can pass integers and reals to your subroutine. Check the inputrec definition in `src/include/types/inputrec.h`

### Index

acc_grps
accelerate
annealing
annealing_npoints
annealing_time
annealing_temp
bd_fric
bd_temp
bDispCorr
comm_mode
comm_grps
compressibility
constraint_algorithm
constraints
cos_acceleration
coulombtype
cpp
define
delta_lambda
disre
disre_weighting
disre_mixed
disre_fc
disre_tau
dt
emstep
emtol
energygrp_excl
energygrps
epsilon_r
ewald_rtol
ewald_geometry
surface_epsilon
E_x
E_xt
E_y
E_yt
E_z
E_zt
fourier_nx
fourier_ny
fourier_nz
fourierspacing
free_energy
freezedim
freezegrps
gen_seed
gen_temp
gen_vel
include
init_lambda
init_step
integrator
ld_seed
lincs_order
lincs_iter
lincs_warnangle
morse
nbfgscorr
nstcgsteep
nstcomm
nstdisreout
nstenergy
nsteps
nstfout
nstlist
nstlog
nstvout
nstxout
nstxtcout
ns_type
optimize_fft
orire
orire_fc
orire_tau
orire_fitgrp
nstorireout
pbc
pcoupl
pcoupltype
pme_order
ref_p
ref_t
rlist
rcoulomb_switch
rcoulomb
rvdw_switch
rvdw
sc_alpha
sc_sigma
shake_tol
table-extension
tau_p
tau_t
tc_grps
tcoupl
tinit
title
unconstrained_start
user1_grps
user2_grps
userint1
userint2
userint3
userint4
userreal1
userreal2
userreal3
userreal4
vdwtype
warnings
xtc_grps
xtc_precision
zero_temp_time

http://www.gromacs.org