generic, preferred for input
:ref:`edi`
essential dynamics constraints input for :ref:`gmx mdrun`
-:ref:`edo`
- essential dynamics constraints output for :ref:`gmx mdrun`
:ref:`eps`
Encapsulated Postscript
:ref:`log`
output from the programs in the <tt>ESSDYN</tt> menu of the
<A HREF="http://www.sander.embl-heidelberg.de/whatif/">WHAT IF</A> program.
-.. _edo:
-
-edo
----
-
-Files with the edo file extension are generated by :ref:`gmx mdrun`
-if Molecular Dynamics is performed with Essential Dynamics
-constraints. Depending on the parameters set in the :ref:`edi`:
-file, edo files may contain projections of positions,
-velocities and forces onto selected eigenvectors during the run as well
-as RMSD values, or information about specific types of constraints.
-Specific results can be extracted from the edo files with standard Unix
-utilities like ``awk``.
-
.. _edr:
edr
energies as generated during your :ref:`gmx mdrun`.
The file can be transformed to a portable energy file (portable
-accross hardware platforms), the :ref:`edr` file using the program
+across hardware platforms), the :ref:`edr` file using the program
:ref:`gmx eneconv`.
See also :ref:`gmx energy`.
itp
---
-The itp file extension stands for include toplogy. These files are included in
+The itp file extension stands for include topology. These files are included in
topology files (with the :ref:`top` extension).
.. _log:
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:
databank file format describes the positions of atoms in a molecular
structure. Coordinates are read from the ATOM and HETATM records,
until the file ends or an ENDMDL record is encountered.
-GROMACS programs can read and write a simlation box in the
+GROMACS programs can read and write a simulation box in the
CRYST1 entry.
The pdb format can also be used as a trajectory format:
-several structures, seperated by ENDMDL, can be read from
+several structures, separated by ENDMDL, can be read from
or written to one file.
Example
+++++++
-An pdb file should look like this::
+A pdb file should look like this::
ATOM 1 H1 LYS 1 14.260 6.590 34.480 1.00 0.00
ATOM 2 H2 LYS 1 13.760 5.000 34.340 1.00 0.00
rtp
---
-The rtp file extension stands for residue toplogy.
+The rtp file extension stands for residue topology.
Such a file is needed by :ref:`gmx pdb2gmx`
to make a GROMACS topology for a protein contained in a :ref:`pdb`
file. The file contains the default interaction type for the 4 bonded
:ref:`gmx pdb2gmx` sets the number exclusions to 3, which
means that interactions between atoms connected by at most 3 bonds are
excluded. Pair interactions are generated for all pairs of atoms which are
-seperated by 3 bonds (except pairs of hydrogens).
+separated by 3 bonds (except pairs of hydrogens).
When more interactions need to be excluded, or some pair interactions should
not be generated, an ``[exclusions]`` field can be added, followed by
-pairs of atom names on seperate lines. All non-bonded and pair interactions
+pairs of atom names on separate lines. All non-bonded and pair interactions
between these atoms will be excluded.
A sample is included below.
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff