Update example old mdp file in user guide.

Update mdp file in user guide. Remove obsolete parameters, and choose parameters
that will not give error and warning by default. Also remove the contents of
mdout.mdp, since the user can easily retrieve that with the given command, and
the file is now much larger. Add note on parameters being dependent on force
fields. Fixes #1774.

Change-Id: I2d5f1cfcf933275f95352c25891ee0792944212c

diff --git a/docs/user-guide/file-formats.rst b/docs/user-guide/file-formats.rst
index 835062578f117196f123d86e222bc9aa77317494..14585262ce77afa583707075a0bc36c44a67541b 100644 (file)
--- a/docs/user-guide/file-formats.rst
+++ b/docs/user-guide/file-formats.rst
@@ -435,222 +435,48 @@ The ordering of the items is not important, but if you enter the same
 thing twice, the **last** is used (:ref:`gmx grompp` gives you a note when
 overriding values). Dashes and underscores on the left hand side are ignored.
 
-The values of the options are reasonable values for a 1 nanosecond
+The values of the options are values for a 1 nanosecond
 MD run of a protein in a box of water.
 
+**Note:** The parameters chosen (*e.g.,* short-range cutoffs) depend on the
+force field being used.
+
 ::
 
-    title                    = Yo
-    cpp                      = /lib/cpp
-    include                  = -I../top
-    define                   =
     integrator               = md
     dt                       = 0.002
     nsteps                   = 500000
-    nstxout                  = 5000
-    nstvout                  = 5000
+
     nstlog                   = 5000
-    nstenergy                = 250
-    nstxout-compressed       = 250
-    compressed-x-grps        = Protein
-    energygrps               = Protein  SOL
-    nstlist                  = 10
-    ns-type                  = grid
-    rlist                    = 0.8
-    coulombtype              = cut-off
-    rcoulomb                 = 1.4
-    rvdw                     = 0.8
-    tcoupl                   = Berendsen
-    tc-grps                  = Protein      SOL
-    tau-t                    = 0.1  0.1
-    ref-t                    = 300  300
-    Pcoupl                   = Berendsen
-    tau-p                    = 1.0
-    compressibility          = 4.5e-5
-    ref-p                    = 1.0
-    gen-vel                  = yes
-    gen-temp                 = 300
-    gen-seed                 = 173529
+    nstenergy                = 5000
+    nstxout-compressed       = 5000
+
+    continuation             = yes
     constraints              = all-bonds
+    constraint-algorithm     = lincs
 
-With this input :ref:`gmx grompp` will produce
-an ``mdout.mdp`` with all the options and descriptions:
+    cutoff-scheme            = Verlet
 
-::
+    coulombtype              = PME
+    rcoulomb                 = 1.0
+    
+    vdwtype                  = Cut-off
+    rvdw                     = 1.0
+    DispCorr                 = EnerPres
 
-    ; VARIOUS PREPROCESSING OPTIONS =
-    title                    = Yo
-    cpp                      = /lib/cpp
-    include                  = -I../top
-    define                   =
+    tcoupl                   = V-rescale
+    tc-grps                  = Protein  SOL
+    tau-t                    = 0.1      0.1
+    ref-t                    = 300      300
 
-    ; RUN CONTROL PARAMETERS =
-    integrator               = md
-    ; start time and timestep in ps =
-    tinit                    = 0
-    dt                       = 0.002
-    nsteps                   = 500000
-    ; number of steps for center of mass motion removal =
-    nstcomm                  = 1
-    comm-grps                =
-
-    ; LANGEVIN DYNAMICS OPTIONS =
-    ; Temperature, friction coefficient (amu/ps) and random seed =
-    bd-temp                  = 300
-    bd-fric                  = 0
-    ld-seed                  = 1993
-
-    ; ENERGY MINIMIZATION OPTIONS =
-    ; Force tolerance and initial step-size =
-    emtol                    = 100
-    emstep                   = 0.01
-    ; Max number of iterations in relax-shells =
-    niter                    = 20
-    ; Frequency of steepest descents steps when doing CG =
-    nstcgsteep               = 1000
-
-    ; OUTPUT CONTROL OPTIONS =
-    ; Output frequency for coords (x), velocities (v) and forces (f) =
-    nstxout                  = 5000
-    nstvout                  = 5000
-    nstfout                  = 0
-    ; Output frequency for energies to log file and energy file =
-    nstlog                   = 5000
-    nstenergy                = 250
-    ; Output frequency and precision for xtc file =
-    nstxout-compressed       = 250
-    compressed-x-precision   = 1000
-    ; This selects the subset of atoms for the xtc file. You can =
-    ; select multiple groups. By default all atoms will be written. =
-    compressed-x-grps        = Protein
-    ; Selection of energy groups =
-    energygrps               = Protein  SOL
-
-    ; NEIGHBORSEARCHING PARAMETERS =
-    ; nblist update frequency =
-    nstlist                  = 10
-    ; ns algorithm (simple or grid) =
-    ns-type                  = grid
-    ; Periodic boundary conditions: xyz or none =
-    pbc                      = xyz
-    ; nblist cut-off         =
-    rlist                    = 0.8
-
-    ; OPTIONS FOR ELECTROSTATICS AND VDW =
-    ; Method for doing electrostatics =
-    coulombtype              = cut-off
-    rcoulomb-switch          = 0
-    rcoulomb                 = 1.4
-    ; Dielectric constant (DC) for cut-off or DC of reaction field =
-    epsilon-r                = 1
-    ; Method for doing Van der Waals =
-    vdw-type                 = Cut-off
-    ; cut-off lengths        =
-    rvdw-switch              = 0
-    rvdw                     = 0.8
-    ; Apply long range dispersion corrections for Energy and Pressure =
-    DispCorr                 = No
-    ; Spacing for the PME/PPPM FFT grid =
-    fourierspacing           = 0.12
-    ; FFT grid size, when a value is 0 fourierspacing will be used =
-    fourier-nx               = 0
-    fourier-ny               = 0
-    fourier-nz               = 0
-    ; EWALD/PME/PPPM parameters =
-    pme-order                = 4
-    ewald-rtol               = 1e-05
-    epsilon-surface          = 0
-
-    ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
-    ; Temperature coupling   =
-    tcoupl                   = Berendsen
-    ; Groups to couple separately =
-    tc-grps                  = Protein      SOL
-    ; Time constant (ps) and reference temperature (K) =
-    tau-t                    = 0.1  0.1
-    ref-t                    = 300  300
-    ; Pressure coupling      =
-    Pcoupl                   = Berendsen
-    Pcoupltype               = Isotropic
-    ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
-    tau-p                    = 1.0
+    pcoupl                   = Parrinello-Rahman
+    tau-p                    = 2.0
     compressibility          = 4.5e-5
     ref-p                    = 1.0
 
-    ; SIMULATED ANNEALING CONTROL =
-    annealing                = no
-    ; Time at which temperature should be zero (ps) =
-    zero-temp-time           = 0
-
-    ; GENERATE VELOCITIES FOR STARTUP RUN =
-    gen-vel                  = yes
-    gen-temp                 = 300
-    gen-seed                 = 173529
-
-    ; OPTIONS FOR BONDS     =
-    constraints              = all-bonds
-    ; Type of constraint algorithm =
-    constraint-algorithm     = Lincs
-    ; Do not constrain the start configuration =
-    unconstrained-start      = no
-    ; Relative tolerance of shake =
-    shake-tol                = 0.0001
-    ; Highest order in the expansion of the constraint coupling matrix =
-    lincs-order              = 4
-    ; Lincs will write a warning to the stderr if in one step a bond =
-    ; rotates over more degrees than =
-    lincs-warnangle          = 30
-    ; Convert harmonic bonds to morse potentials =
-    morse                    = no
-
-    ; NMR refinement stuff  =
-    ; Distance restraints type: No, Simple or Ensemble =
-    disre                    = No
-    ; Force weighting of pairs in one distance restraint: Equal or Conservative =
-    disre-weighting          = Equal
-    ; Use sqrt of the time averaged times the instantaneous violation =
-    disre-mixed              = no
-    disre-fc                 = 1000
-    disre-tau                = 0
-    ; Output frequency for pair distances to energy file =
-    nstdisreout              = 100
-
-    ; Free energy control stuff =
-    free-energy              = no
-    init-lambda              = 0
-    delta-lambda             = 0
-    sc-alpha                 = 0
-    sc-sigma                 = 0.3
-
-    ; Non-equilibrium MD stuff =
-    acc-grps                 =
-    accelerate               =
-    freezegrps               =
-    freezedim                =
-    cos-acceleration         = 0
-    energygrp-excl           =
-
-    ; Electric fields       =
-    ; Format is number of terms (int) and for all terms an amplitude (real) =
-    ; and a phase angle (real) =
-    E-x                      =
-    E-xt                     =
-    E-y                      =
-    E-yt                     =
-    E-z                      =
-    E-zt                     =
-
-    ; User defined thingies =
-    user1-grps               =
-    user2-grps               =
-    userint1                 = 0
-    userint2                 = 0
-    userint3                 = 0
-    userint4                 = 0
-    userreal1                = 0
-    userreal2                = 0
-    userreal3                = 0
-    userreal4                = 0
+With this input :ref:`gmx grompp` will produce a commented file with the default name
+``mdout.mdp``. That file will contain the above options, as well as all other
+options not explicitly set, showing their default values.
 
 .. _mtx: