1 Answers to frequently asked questions (FAQs)
2 ============================================
4 .. _reference manual: `gmx-manual-parent-dir`_
6 .. Migrated from old website
12 Questions regarding |Gromacs| installation
13 ------------------------------------------
15 #. Do I need to compile all utilities with MPI?
17 With one rarely-used exception (:ref:`pme_error <gmx pme_error>`), only the
18 :ref:`mdrun <gmx mdrun>` binary is able to use the :ref:`MPI <mpi-support>`
19 parallelism. So you only need to use the ``-DGMX_MPI=on`` flag
20 when :ref:`configuring <configure-cmake>` for a build intended to run
21 the main simulation engine :ref:`mdrun <gmx mdrun>`.
24 #. Should my version be compiled using double precision?
26 In general, |Gromacs| only needs to be build in its default mixed-precision mode.
27 For more details, see the discussion in Chapter 2 of the `reference manual`_.
28 Sometimes, usage may also depend on your target system, and should be decided
29 upon according to the :ref:`individual instructions <gmx-special-build>`.
31 Questions concerning system preparation and preprocessing
32 ---------------------------------------------------------
34 #. Where can I find a solvent :ref:`coordinate file <gmx-structure-files>` for use with :ref:`solvate <gmx solvate>`?
36 Suitable equilibrated boxes of solvent :ref:`structure files <gmx-structure-files>` can be found
37 in the ``$GMXDIR/share/gromacs/top`` directory. That location will be searched by default
38 by :ref:`solvate <gmx solvate>`, for example by using ``-cs spc216.gro`` as an argument.
39 Other solvent boxes can be prepared by the user as described
40 on the manual page for :ref:`solvate <gmx solvate>` and elsewhere.
41 Note that suitable topology files will be needed for the solvent boxes to be useful in
42 :ref:`grompp <gmx grompp>`. These are available for some force fields, and may be
43 found in the respective subfolder of ``$GMXDIR/share/gromacs/top``.
45 #. How to prevent :ref:`solvate <gmx solvate>` from placing waters in undesired places?
47 Water placement is generally well behaved when solvating proteins, but can be difficult when setting up
48 membrane or micelle simulations. In those cases, waters may be placed in between the
49 alkyl chains of the lipids, leading to problems later :ref:`during the simulation <blowing-up>`.
50 You can either remove those waters by hand (and do the accounting for molecule types in the
51 :ref:`topology <top>` file), or set up a local copy of the ``vdwradii.dat`` file from the ``$GMXLIB``
52 directory, specific for your project and located in your working directory. In it, you can
53 increase the vdW radius of the atoms, to suppress such interstitial insertions.
54 Recommended e.g. at a common `tutorial`_ is the use of 0.375 instead of 0.15.
56 .. _tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
58 #. How do I provide multiple definitions of bonds / dihedrals in a topology?
60 You can add additional bonded terms beyond those that are normally defined for a residue (e.g. when defining
61 a special ligand) by including additional copies of the respective lines under the
62 ``[ bonds ]``, ``[ pairs ]``, ``[ angles ]`` and ``[ dihedrals ]`` sections in the ``[ moleculetype ]``
63 section for your molecule, found either in the :ref:`itp` file
64 or the :ref:`topology <top>` file. This will **add** those extra terms to the potential energy evaluation,
65 but **will not** remove the previous ones. So be careful with duplicate entries. Also keep in mind that this **does not**
66 apply to duplicated entries for ``[ bondtypes ]``, ``[ angletypes ]``, or ``[ dihedraltypes ]``, in force-field
67 definition files, where duplicates overwrite the previous values.
69 #. Do I really need a :ref:`gro` file?
71 The :ref:`gro` file is used in |Gromacs| as a unified :ref:`structure file <gmx-structure-files>` format
72 that can be read by all utilities. The large majority of |Gromacs| routines can also use other file
73 types such as :ref:`pdb`, with the limitations that no velocities are available in :ref:`this case <gmx-need-for-gro>`.
74 If you need a text-based format with more digits of precision, the :ref:`g96` format is suitable and supported.
76 #. Do I always need to run :ref:`pdb2gmx <gmx pdb2gmx>` when I already produced an :ref:`itp` file elsewhere?
78 You don't need to prepare additional files if you already have all :ref:`itp` and :ref:`top` files prepared through other tools.
80 Examples for those are `CHARMM-GUI <http://www.charmm-gui.org/>`__, `ATB (Automated Topology Builder) <https://atb.uq.edu.au/>`__,
81 `pmx <http://pmx.mpibpc.mpg.de/instructions.html>`__. and `PRODRG <http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg>`__.
83 #. How can I build in missing atoms?
85 |Gromacs| has no support for building coordinates of missing non-hydrogen atoms. If your system is missing some part,
86 you will have to add the missing pieces using external programs to avoid the :ref:`missing atom <gmx-atom-missing>`
87 error. This can be done using programs such as `Chimera <https://www.cgl.ucsf.edu/chimera/>`__ in combination
88 with `Modeller <https://salilab.org/modeller/>`__, `Swiss PDB Viewer <https://spdbv.vital-it.ch/>`__,
89 `Maestro <https://www.schrodinger.com/maestro>`__. **Do not run** a simulation that had missing atoms unless
90 you know exactly why it will be stable.
92 #. Why is the total charge of my system not an integer like it should be?
94 In :ref:`floating point <gmx-floating-point>` math, real numbers can not be displayed to arbitrary precision
95 (for more on this, see e.g. `Wikipedia <https://en.wikipedia.org/wiki/Floating-point_arithmetic>`__). This means
96 that very small differences to the final integer value will persist, and |Gromacs| will not lie to you and
97 round those values up or down. If your charge differs from the integer value by a larger amount, e.g. at least
98 0.01, this usually means that something went wrong during your system preparation
100 Questions regarding simulation methodology
101 ------------------------------------------
103 #. Should I couple a handful of ions to their own temperature-coupling bath?
105 **No**. You need to consider the minimal size of your
106 temperature coupling groups, as explained in :ref:`gmx-thermostats` and more
107 specifically in :ref:`gmx-thermostats-dont`, as well as the implementation
108 of your chosen thermostat as described in the `reference manual`_.
110 #. Why do my grompp restarts always start from time zero?
112 You can choose different values for :mdp:`tinit` and :mdp:`init-step`.
114 .. todo:: Add "Continuing simulations" content (label: gmx-cont-simulation) and link.
116 e.g. ``:ref:`Continuing simulations <gmx-cont-simulation>`.``
118 #. Why can't I do conjugate gradient minimization with constraints?
120 Minimization with the conjugate gradient scheme can not be performed with constraints
121 as described in the `reference manual`_, and some additional information
122 on `Wikipedia <https://en.wikipedia.org/wiki/Conjugate_gradient_method>`__.
124 #. How do I hold atoms in place in my energy minimization or simulation?
126 Groups may be frozen in place using ``freeze groups`` (see the `reference manual`_).
127 It is more common to use a set of position
128 restraints, to place penalties on movement of the atoms. Files that control this
129 kind of behaviour can be created using :ref:`genrestr <gmx genrestr>`.
131 #. How do I extend a completed a simulation to longer times?
133 Please see the section on :ref:`managing long simulations`.
134 You can either prepare a new :ref:`mdp` file, or extend the simulation time
135 in the original :ref:`tpr` file using :ref:`convert-tpr <gmx convert-tpr>`.
137 .. todo:: #. How do I complete a crashed simulation?
139 Need gmx-cont-crash doc target.
143 This can be easily achieved using the checkpoint reading
144 :ref:`available <gmx-cont-crash>` in |Gromacs| versions newer than 4.
146 .. todo:: #. How can I do a simulation at constant pH?
148 Need gmx-howto-cph doc target.
152 This is a rather large topic, and you should at least read the short
153 :ref:`Constant pH How-To <gmx-howto-cph>` and all of the literature
154 included there to get an overview over the topic.
156 #. How should I compute a single-point energy?
158 This is best achieved with the ``-rerun`` option to :ref:`mdrun <gmx mdrun>`.
159 See the :ref:`single-point energy` section.
161 Parameterization and Force Fields
162 ---------------------------------
164 #. I want to simulate a molecule (protein, DNA, etc.) which complexes with
165 various transition metal ions, iron-sulfur clusters, or other exotic species.
166 Parameters for these exotic species aren't available in force field X.
169 First, you should consider how well :ref:`MD <gmx-md>` will actually describe your
170 system (e.g. see some of the `recent literature <https://dx.doi.org/10.1021%2Facs.chemrev.6b00440>`__).
171 Many species are infeasible to model without either atomic polarizability, or QM treatments.
172 Then you need to prepare your own set of parameters and add a new residue
173 to your :ref:`force field <gmx-force-field>` of choice. Then you will have to validate that
174 your system behaves in a physical way, before continuing your simulation studies. You could
175 also try to build a more simplified model that does not rely on the complicated additions,
176 as long as it still represents the correct *real* object in the laboratory.
178 #. Should I take parameters from one force field and apply them inside another that is missing them?
180 **NO**. Molecules parametrized for a given
181 :ref:`force field <gmx-force-field>` will not behave in a physical manner when interacting with
182 other molecules that have been parametrized according to different standards. If your
183 required molecule is not included in the force field you need to use, you will
184 have to parametrize it yourself according to the methodology of this force field.
186 Analysis and Visualization
187 --------------------------
189 .. todo:: #. How do I visualize a trajectory?
191 gmx-howto-visualize doc target:
195 Use one of the number of different programs that can visualize
196 coordinate :ref:`files and trajectories <gmx-howto-visualize>`.
198 #. Why am I seeing bonds being created when I watch the trajectory?
200 Most visualization softwares determine the bond status of atoms depending
201 on a set of predefined distances. So the bonding pattern created by them
202 might not be the one defined in your :ref:`topology <top>` file. What
203 matters is the information encoded in there. If the software has read
204 a :ref:`tpr <tpr>` file, then the information is in reliable agreement
205 with the topology you supplied to :ref:`grompp <gmx grompp>`.
207 #. When visualizing a trajectory from a simulation using PBC, why are there holes or my peptide leaving the simulation box?
209 Those holes and molecules moving around are just a result of molecules
210 ranging over the :ref:`box boundaries and wrapping around <gmx-pbc>`,
211 and are not a reason for concern. You can fix the visualization using :ref:`trjconv <gmx trjconv>`
212 to prepare the structure for analysis.
214 #. Why is my total simulation time not an integer like it should be?
216 As the simulation time is calculated using :ref:`floating point arithmetic <gmx-floating-point>`,
217 rounding errors can occur but are not of concern.