| VERSION 3.0 |
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.
-I/home/john/my_lib -I../more_lib
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 gradient work and will allow steepest descent to minimize further.
-DPOSRE
Will tell grompp to include posre.itp into your topology, used for position restraints.
starting time for your run (only makes sense for integrators md, sd and bd)
time step for integration (only makes sense for integrators md, sd and bd)
maximum number of steps to integrate
if positive: frequency for center of mass motion removal
if negative: frequency for center of mass motion and rotational motion removal (should only be used for vacuum simulations)
group(s) for center of mass motion removal, default is the whole system, rotation removal can only be done on the whole system
temperature in Brownian dynamics run (controls thermal noise level). When bd_fric=0, ref_t is used instead.
Brownian dynamics friction coefficient. When bd_fric=0, the friction coefficient for each particle is calculated as mass/tau_t.
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
the minimization is converged when the maximum force is smaller than this value
initial step-size
frequency of performing 1 steepest descent step while doing conjugate gradient energy minimization.
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.
maximum number of iterations for optimizing the shell positions.
frequency to write coordinates to output trajectory file, the last coordinates are always written
frequency to write velocities to output trajectory, the last velocities are always written
frequency to write forces to output trajectory.
frequency to write energies to log file, the last energies are always written
frequency to write energies to energy file, the last energies are always written
frequency to write coordinates to xtc trajectory
precision to write to xtc trajectory
group(s) to write to xtc trajectory, default the whole system is written (if nstxtcout is larger than zero)
group(s) to write to energy file
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.
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.
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.
cut-off distance for the short-range neighbor list
where to start switching the Coulomb potential
distance for the Coulomb cut-off
dielectric constant
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.
User
mdrun will now expect to find two files with user-defined functions: rtab.xvg for Repulsion, dtab.xvg for Dispersion. These files should contain 5 columns: the x value, f(x), -f(1)(x), f(2)(x) and -f(3)(x), where f(n)(x) denotes the nth derivative of function f(x) with respect to x. The x should run from 0 [nm] to rlist+0.5 [nm], with a spacing of 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. When you want to use LJ correction, make sure that rvdw corresponds to the cut-off in the user-defined function.
where to start switching the LJ potential
distance for the LJ or Buckingham cut-off
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
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*.
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.
Interpolation order for PME. 4 equals cubic interpolation. You might try 6/8/10 when running in parallel and simultaneously decrease grid dimension.
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.
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.
time constant for coupling (one for each group in tc_grps)
reference temperature for coupling (one for each group in tc_grps)
time constant for coupling
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].
reference pressure for coupling
time at which temperature will be zero (can be negative). Temperature during the run can be seen as a straight line going through T=ref_t [K] at t=0 [ps], and T=0 [K] at t=zero_temp_time [ps]. Look in our FAQ for a schematic graph of temperature versus time.
temperature for Maxwell distribution
used to initialize random generator for random velocities, when gen_seed is set to -1, the seed is calculated as (time() + getpid()) % 1000000
relative tolerance for shake
Highest order in the expansion of the constraint coupling matrix. lincs_order is also used for the number of Lincs iterations during energy minimization, only one iteration is used in MD.
maximum angle that a bond can rotate before Lincs will complain
no
bonds are represented by a harmonic potential
yes
bonds are represented by a Morse potential
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.
force constant for distance restraints, which is multiplied by a (possibly) different factor for each restraint
time constant for distance restraints running average
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)
starting value for lambda
increase per time step for lambda
the soft-core parameter, a value of 0 results in linear interpolation of the LJ and Coulomb interactions
the soft-core sigma for particles which have a C6 or C12 parameter equal to zero
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
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).
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.
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).
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.
not implemented yet
These you can use if you hack out code. You can pass integers and reals to your subroutine. Check the inputrec definition in src/include/types/inputrec.h
accelerate
annealing
bd_fric
bd_temp
bDispCorr
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
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
integrator
ld_seed
lincs_order
lincs_warnangle
morse
nstcgsteep
nstcomm
nstdisreout
nstenergy
nsteps
nstfout
nstlist
nstlog
nstvout
nstxout
nstxtcout
ns_type
optimize_fft
pbc
pcoupl
pcoupltype
pme_order
ref_p
ref_t
rlist
rcoulomb_switch
rcoulomb
rvdw_switch
rvdw
sc_alpha
sc_sigma
shake_tol
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