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Answers to frequently asked questions (FAQs)
============================================

.. _reference manual: `gmx-manual-parent-dir`_

.. Migrated from old website

.. toctree::
   :maxdepth: 2
   :hidden:

Questions regarding |Gromacs| installation
------------------------------------------

#. Do I need to compile all utilities with MPI?
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   With one rarely-used exception (:ref:`pme_error <gmx pme_error>`), only the
   :ref:`mdrun <gmx mdrun>` binary is able to use the :ref:`MPI <mpi-support>`
   parallelism. So you only need to use the ``-DGMX_MPI=on`` flag
   when :ref:`configuring <configure-cmake>` for a build intended to run
   the main simulation engine :ref:`mdrun <gmx mdrun>`.


#. Should my version be compiled using double precision?

   In general, |Gromacs| only needs to be build in its default mixed-precision mode.
   For more details, see the discussion in Chapter 2 of the `reference manual`_.
   Sometimes, usage may also depend on your target system, and should be decided
   upon according to the :ref:`individual instructions <gmx-special-build>`.

Questions concerning system preparation and preprocessing
---------------------------------------------------------

#. Where can I find a solvent :ref:`coordinate file <gmx-structure-files>` for use with :ref:`solvate <gmx solvate>`?

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   Suitable equilibrated boxes of solvent :ref:`structure files <gmx-structure-files>` can be found
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   in the ``$GMXDIR/share/gromacs/top`` directory. That location will be searched by default
   by :ref:`solvate <gmx solvate>`, for example by using ``-cs spc216.gro`` as an argument.
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   Other solvent boxes can be prepared by the user as described
   on the manual page for :ref:`solvate <gmx solvate>` and elsewhere.
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   Note that suitable topology files will be needed for the solvent boxes to be useful in
   :ref:`grompp <gmx grompp>`. These are available for some force fields, and may be
   found in the respective subfolder of ``$GMXDIR/share/gromacs/top``.

#. How to prevent :ref:`solvate <gmx solvate>` from placing waters in undesired places?

   Water placement is generally well behaved when solvating proteins, but can be difficult when setting up
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   membrane or micelle simulations. In those cases, waters may be placed in between the
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   alkyl chains of the lipids, leading to problems later :ref:`during the simulation <blowing-up>`.
   You can either remove those waters by hand (and do the accounting for molecule types in the
   :ref:`topology <top>` file), or set up a local copy of the ``vdwradii.dat`` file from the ``$GMXLIB``
   directory, specific for your project and located in your working directory. In it, you can
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   increase the vdW radius of the atoms, to suppress such interstitial insertions.
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   Recommended e.g. at a common `tutorial`_ is the use of 0.375 instead of 0.15.

.. _tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html

#. How do I provide multiple definitions of bonds / dihedrals in a topology?

   You can add additional bonded terms beyond those that are normally defined for a residue (e.g. when defining
   a special ligand) by including additional copies of the respective lines under the
   ``[ bonds ]``, ``[ pairs ]``, ``[ angles ]`` and ``[ dihedrals ]`` sections in the ``[ moleculetype ]``
   section for your molecule, found either in the :ref:`itp` file
   or the :ref:`topology <top>` file. This will **add** those extra terms to the potential energy evaluation,
   but **will not** remove the previous ones. So be careful with duplicate entries. Also keep in mind that this **does not**
   apply to duplicated entries for ``[ bondtypes ]``, ``[ angletypes ]``, or ``[ dihedraltypes ]``, in force-field
   definition files, where duplicates overwrite the previous values.

#. Do I really need a :ref:`gro` file?

   The :ref:`gro` file is used in |Gromacs| as a unified :ref:`structure file <gmx-structure-files>` format
   that can be read by all utilities. The large majority of |Gromacs| routines can also use other file
   types such as :ref:`pdb`, with the limitations that no velocities are available in :ref:`this case <gmx-need-for-gro>`.
   If you need a text-based format with more digits of precision, the :ref:`g96` format is suitable and supported.

#. Do I always need to run :ref:`pdb2gmx <gmx pdb2gmx>` when I already produced an :ref:`itp` file elsewhere?

   You don't need to prepare additional files if you already have all :ref:`itp` and :ref:`top` files prepared through other tools.

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   Examples for those are `CHARMM-GUI <http://www.charmm-gui.org/>`__, `ATB (Automated Topology Builder) <https://atb.uq.edu.au/>`__,
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   `pmx <http://pmx.mpibpc.mpg.de/instructions.html>`__. and `PRODRG <http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg>`__.

#. How can I build in missing atoms?

   |Gromacs| has no support for building coordinates of missing non-hydrogen atoms. If your system is missing some part,
   you will have to add the missing pieces using external programs to avoid the :ref:`missing atom <gmx-atom-missing>`
   error. This can be done using programs such as `Chimera <https://www.cgl.ucsf.edu/chimera/>`__ in combination
   with `Modeller <https://salilab.org/modeller/>`__, `Swiss PDB Viewer <https://spdbv.vital-it.ch/>`__,
   `Maestro <https://www.schrodinger.com/maestro>`__. **Do not run** a simulation that had missing atoms unless
   you know exactly why it will be stable.

#. Why is the total charge of my system not an integer like it should be?

   In :ref:`floating point <gmx-floating-point>` math, real numbers can not be displayed to arbitrary precision
   (for more on this, see e.g. `Wikipedia <https://en.wikipedia.org/wiki/Floating-point_arithmetic>`__). This means
   that very small differences to the final integer value will persist, and |Gromacs| will not lie to you and
   round those values up or down. If your charge differs from the integer value by a larger amount, e.g. at least
   0.01, this usually means that something went wrong during your system preparation

Questions regarding simulation methodology
------------------------------------------

#.  Should I couple a handful of ions to their own temperature-coupling bath?

    **No**. You need to consider the minimal size of your
    temperature coupling groups, as explained in :ref:`gmx-thermostats` and more
    specifically in :ref:`gmx-thermostats-dont`, as well as the implementation
    of your chosen thermostat as described in the `reference manual`_.

#.  Why do my grompp restarts always start from time zero?

    You can choose different values for :mdp:`tinit` and :mdp:`init-step`.

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    .. TODO make links work :ref:`Continuing simulations <gmx-cont-simulation>`.
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#.  Why can't I do conjugate gradient minimization with constraints?

    Minimization with the conjugate gradient scheme can not be performed with constraints
    as described in the `reference manual`_, and some additional information
    on `Wikipedia <https://en.wikipedia.org/wiki/Conjugate_gradient_method>`__.

#.  How do I hold atoms in place in my energy minimization or simulation?

    Groups may be frozen in place using ``freeze groups`` (see the `reference manual`_).
    It is more common to use a set of position
    restraints, to place penalties on movement of the atoms. Files that control this
    kind of behaviour can be created using :ref:`genrestr <gmx genrestr>`.

#.  How do I extend a completed a simulation to longer times?

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    Please see the section on :ref:`managing long simulations`.
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    You can either prepare a new :ref:`mdp` file, or extend the simulation time
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    in the original :ref:`tpr` file using :ref:`convert-tpr <gmx convert-tpr>`.
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    .. TODO #.  How do I complete a crashed simulation?
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    .. This can be easily achieved using the checkpoint reading
       :ref:`available <gmx-cont-crash>` in |Gromacs| versions newer than 4.
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    .. TODO #.  How can I do a simulation at constant pH?
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    .. This is a rather large topic, and you should at least read the short
       :ref:`Constant pH How-To <gmx-howto-cph>` and all of the literature
       included there to get an overview over the topic.
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#.  How should I compute a single-point energy?

    This is best achieved with the ``-rerun`` option to :ref:`mdrun <gmx mdrun>`.
    See the :ref:`single-point energy` section.

Parameterization and Force Fields
---------------------------------

#.  I want to simulate a molecule (protein, DNA, etc.) which complexes with
    various transition metal ions, iron-sulfur clusters, or other exotic species.
    Parameters for these exotic species aren't available in force field X.
    What should I do?

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    First, you should consider how well :ref:`MD <gmx-md>` will actually describe your
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    system (e.g. see some of the `recent literature <https://dx.doi.org/10.1021%2Facs.chemrev.6b00440>`__).
    Many species are infeasible to model without either atomic polarizability, or QM treatments.
    Then you need to prepare your own set of parameters and add a new residue
    to your :ref:`force field <gmx-force-field>` of choice. Then you will have to validate that
    your system behaves in a physical way, before continuing your simulation studies. You could
    also try to build a more simplified model that does not rely on the complicated additions,
    as long as it still represents the correct *real* object in the laboratory.

#.  Should I take parameters from one force field and apply them inside another that is missing them?

    **NO**. Molecules parametrized for a given
    :ref:`force field <gmx-force-field>` will not behave in a physical manner when interacting with
    other molecules that have been parametrized according to different standards. If your
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    required molecule is not included in the force field you need to use, you will
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    have to parametrize it yourself according to the methodology of this force field.

Analysis and Visualization
--------------------------

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    .. TODO #.  How do I visualize a trajectory?
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    .. Use one of the number of different programs that can visualize
       coordinate :ref:`files and trajectories <gmx-howto-visualize>`.
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#.  Why am I seeing bonds being created when I watch the trajectory?

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    Most visualization softwares determine the bond status of atoms depending
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    on a set of predefined distances. So the bonding pattern created by them
    might not be the one defined in your :ref:`topology <top>` file. What
    matters is the information encoded in there. If the software has read
    a :ref:`tpr <tpr>` file, then the information is in reliable agreement
    with the topology you supplied to :ref:`grompp <gmx grompp>`.

#.  When visualizing a trajectory from a simulation using PBC, why are there holes or my peptide leaving the simulation box?

    Those holes and molecules moving around are just a result of molecules
    ranging over the :ref:`box boundaries and wrapping around <gmx-pbc>`,
    and are not a reason for concern. You can fix the visualization using :ref:`trjconv <gmx trjconv>`
    to prepare the structure for analysis.

#.  Why is my total simulation time not an integer like it should be?

    As the simulation time is calculated using :ref:`floating point arithmetic <gmx-floating-point>`,
    rounding errors can occur but are not of concern.