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
18 :ref:`mdrun <gmx mdrun>` 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>`. Generally that
22 is desirable when running on a multi-node cluster, and necessary
23 when using multi-simulation algorithms. Usually also installing a
24 build of GROMACS configured without MPI is convenient for users.
27 #. Should my version be compiled using double precision?
29 In general, |Gromacs| only needs to be build in its default mixed-precision mode.
30 For more details, see the discussion in Chapter 2 of the `reference manual`_.
31 Sometimes, usage may also depend on your target system, and should be decided
32 upon according to the :ref:`individual instructions <gmx-special-build>`.
34 Questions concerning system preparation and preprocessing
35 ---------------------------------------------------------
37 #. Where can I find a solvent :ref:`coordinate file <gmx-structure-files>` for use with :ref:`solvate <gmx solvate>`?
39 Suitable equilibrated boxes of solvent :ref:`structure files <gmx-structure-files>` can be found
40 in the ``$GMXDIR/share/gromacs/top`` directory. That location will be searched by default
41 by :ref:`solvate <gmx solvate>`, for example by using ``-cs spc216.gro`` as an argument.
42 Other solvent boxes can be prepared by the user as described
43 on the manual page for :ref:`solvate <gmx solvate>` and elsewhere.
44 Note that suitable topology files will be needed for the solvent boxes to be useful in
45 :ref:`grompp <gmx grompp>`. These are available for some force fields, and may be
46 found in the respective subfolder of ``$GMXDIR/share/gromacs/top``.
48 #. How to prevent :ref:`solvate <gmx solvate>` from placing waters in undesired places?
50 Water placement is generally well behaved when solvating proteins, but can be difficult when setting up
51 membrane or micelle simulations. In those cases, waters may be placed in between the
52 alkyl chains of the lipids, leading to problems later :ref:`during the simulation <blowing-up>`.
53 You can either remove those waters by hand (and do the accounting for molecule types in the
54 :ref:`topology <top>` file), or set up a local copy of the ``vdwradii.dat`` file from the ``$GMXLIB``
55 directory, specific for your project and located in your working directory. In it, you can
56 increase the vdW radius of the atoms, to suppress such interstitial insertions.
57 Recommended e.g. at a common `tutorial`_ is the use of 0.375 instead of 0.15.
59 .. _tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
61 #. How do I provide multiple definitions of bonds / dihedrals in a topology?
63 You can add additional bonded terms beyond those that are normally defined for a residue (e.g. when defining
64 a special ligand) by including additional copies of the respective lines under the
65 ``[ bonds ]``, ``[ pairs ]``, ``[ angles ]`` and ``[ dihedrals ]`` sections in the ``[ moleculetype ]``
66 section for your molecule, found either in the :ref:`itp` file
67 or the :ref:`topology <top>` file. This will **add** those extra terms to the potential energy evaluation,
68 but **will not** remove the previous ones. So be careful with duplicate entries. Also keep in mind that this **does not**
69 apply to duplicated entries for ``[ bondtypes ]``, ``[ angletypes ]``, or ``[ dihedraltypes ]``, in force-field
70 definition files, where duplicates overwrite the previous values.
72 #. Do I really need a :ref:`gro` file?
74 The :ref:`gro` file is used in |Gromacs| as a unified :ref:`structure file <gmx-structure-files>` format
75 that can be read by all utilities. The large majority of |Gromacs| routines can also use other file
76 types such as :ref:`pdb`, with the limitations that no velocities are available in :ref:`this case <gmx-need-for-gro>`.
77 If you need a text-based format with more digits of precision, the :ref:`g96` format is suitable and supported.
79 #. Do I always need to run :ref:`pdb2gmx <gmx pdb2gmx>` when I already produced an :ref:`itp` file elsewhere?
81 You don't need to prepare additional files if you already have all :ref:`itp` and :ref:`top` files prepared through other tools.
83 Examples for those are `CHARMM-GUI <http://www.charmm-gui.org/>`__, `ATB (Automated Topology Builder) <https://atb.uq.edu.au/>`__,
84 `pmx <http://pmx.mpibpc.mpg.de/instructions.html>`__. and `PRODRG <http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg>`__.
86 #. How can I build in missing atoms?
88 |Gromacs| has no support for building coordinates of missing non-hydrogen atoms. If your system is missing some part,
89 you will have to add the missing pieces using external programs to avoid the :ref:`missing atom <gmx-atom-missing>`
90 error. This can be done using programs such as `Chimera <https://www.cgl.ucsf.edu/chimera/>`__ in combination
91 with `Modeller <https://salilab.org/modeller/>`__, `Swiss PDB Viewer <https://spdbv.vital-it.ch/>`__,
92 `Maestro <https://www.schrodinger.com/maestro>`__. **Do not run** a simulation that had missing atoms unless
93 you know exactly why it will be stable.
95 #. Why is the total charge of my system not an integer like it should be?
97 In :ref:`floating point <gmx-floating-point>` math, real numbers can not be displayed to arbitrary precision
98 (for more on this, see e.g. `Wikipedia <https://en.wikipedia.org/wiki/Floating-point_arithmetic>`__). This means
99 that very small differences to the final integer value will persist, and |Gromacs| will not lie to you and
100 round those values up or down. If your charge differs from the integer value by a larger amount, e.g. at least
101 0.01, this usually means that something went wrong during your system preparation
103 Questions regarding simulation methodology
104 ------------------------------------------
106 #. Should I couple a handful of ions to their own temperature-coupling bath?
108 **No**. You need to consider the minimal size of your
109 temperature coupling groups, as explained in :ref:`gmx-thermostats` and more
110 specifically in :ref:`gmx-thermostats-dont`, as well as the implementation
111 of your chosen thermostat as described in the `reference manual`_.
113 #. Why do my grompp restarts always start from time zero?
115 You can choose different values for :mdp:`tinit` and :mdp:`init-step`.
117 .. todo:: Add "Continuing simulations" content (label: gmx-cont-simulation) and link.
119 e.g. ``:ref:`Continuing simulations <gmx-cont-simulation>`.``
121 #. Why can't I do conjugate gradient minimization with constraints?
123 Minimization with the conjugate gradient scheme can not be performed with constraints
124 as described in the `reference manual`_, and some additional information
125 on `Wikipedia <https://en.wikipedia.org/wiki/Conjugate_gradient_method>`__.
127 #. How do I hold atoms in place in my energy minimization or simulation?
129 Groups may be frozen in place using ``freeze groups`` (see the `reference manual`_).
130 It is more common to use a set of position
131 restraints, to place penalties on movement of the atoms. Files that control this
132 kind of behaviour can be created using :ref:`genrestr <gmx genrestr>`.
134 #. How do I extend a completed a simulation to longer times?
136 Please see the section on :ref:`managing long simulations`.
137 You can either prepare a new :ref:`mdp` file, or extend the simulation time
138 in the original :ref:`tpr` file using :ref:`convert-tpr <gmx convert-tpr>`.
140 .. todo:: #. How do I complete a crashed simulation?
142 Need gmx-cont-crash doc target.
146 This can be easily achieved using the checkpoint reading
147 :ref:`available <gmx-cont-crash>` in |Gromacs| versions newer than 4.
149 .. todo:: #. How can I do a simulation at constant pH?
151 Need gmx-howto-cph doc target.
155 This is a rather large topic, and you should at least read the short
156 :ref:`Constant pH How-To <gmx-howto-cph>` and all of the literature
157 included there to get an overview over the topic.
159 #. How should I compute a single-point energy?
161 This is best achieved with the ``-rerun`` option to :ref:`mdrun <gmx mdrun>`.
162 See the :ref:`single-point energy` section.
164 Parameterization and Force Fields
165 ---------------------------------
167 #. I want to simulate a molecule (protein, DNA, etc.) which complexes with
168 various transition metal ions, iron-sulfur clusters, or other exotic species.
169 Parameters for these exotic species aren't available in force field X.
172 First, you should consider how well :ref:`MD <gmx-md>` will actually describe your
173 system (e.g. see some of the `recent literature <https://dx.doi.org/10.1021%2Facs.chemrev.6b00440>`__).
174 Many species are infeasible to model without either atomic polarizability, or QM treatments.
175 Then you need to prepare your own set of parameters and add a new residue
176 to your :ref:`force field <gmx-force-field>` of choice. Then you will have to validate that
177 your system behaves in a physical way, before continuing your simulation studies. You could
178 also try to build a more simplified model that does not rely on the complicated additions,
179 as long as it still represents the correct *real* object in the laboratory.
181 #. Should I take parameters from one force field and apply them inside another that is missing them?
183 **NO**. Molecules parametrized for a given
184 :ref:`force field <gmx-force-field>` will not behave in a physical manner when interacting with
185 other molecules that have been parametrized according to different standards. If your
186 required molecule is not included in the force field you need to use, you will
187 have to parametrize it yourself according to the methodology of this force field.
189 Analysis and Visualization
190 --------------------------
192 .. todo:: #. How do I visualize a trajectory?
194 gmx-howto-visualize doc target:
198 Use one of the number of different programs that can visualize
199 coordinate :ref:`files and trajectories <gmx-howto-visualize>`.
201 #. Why am I seeing bonds being created when I watch the trajectory?
203 Most visualization softwares determine the bond status of atoms depending
204 on a set of predefined distances. So the bonding pattern created by them
205 might not be the one defined in your :ref:`topology <top>` file. What
206 matters is the information encoded in there. If the software has read
207 a :ref:`tpr <tpr>` file, then the information is in reliable agreement
208 with the topology you supplied to :ref:`grompp <gmx grompp>`.
210 #. When visualizing a trajectory from a simulation using PBC, why are there holes or my peptide leaving the simulation box?
212 Those holes and molecules moving around are just a result of molecules
213 ranging over the :ref:`box boundaries and wrapping around <gmx-pbc>`,
214 and are not a reason for concern. You can fix the visualization using :ref:`trjconv <gmx trjconv>`
215 to prepare the structure for analysis.
217 #. Why is my total simulation time not an integer like it should be?
219 As the simulation time is calculated using :ref:`floating point arithmetic <gmx-floating-point>`,
220 rounding errors can occur but are not of concern.