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If you did not obtain your coordinates file from a protein database, but instead created it yourself, most likely you will need to create a residue template file ({{ic|.rtp}}) for your molecule as well as update the {{ic|.pdb}} file. An example {{ic|.rtp}} file for OPLS methane is found [https://gist.github.com/anonymous/a8e862c29a8c50f374f0#file-methane-rtp here] with its corresponding {{ic|.pdb}} file [https://gist.githubusercontent.com/wesbarnett/9814526/raw/fed66209a702645b1e0871396f58de6b8b610516/methane-1.pdb here]. The {{ic|.rtp}} file must be placed in the force field directory for the force field you are going to use.
If you did not obtain your coordinates file from a protein database, but instead created it yourself, most likely you will need to create a residue template file ({{ic|.rtp}}) for your molecule as well as update the {{ic|.pdb}} file. An example {{ic|.rtp}} file for OPLS methane is found [https://gist.github.com/anonymous/a8e862c29a8c50f374f0#file-methane-rtp here] with its corresponding {{ic|.pdb}} file [https://gist.githubusercontent.com/wesbarnett/9814526/raw/fed66209a702645b1e0871396f58de6b8b610516/methane-1.pdb here]. The {{ic|.rtp}} file must be placed in the force field directory for the force field you are going to use.
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[[#See_also|See below]] for alternative ways to generate or obtain topologies.
==== Box creation ====
==== Box creation ====
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=== Analysis ===
=== Analysis ===
−
−
==== Built-in tools ====
GROMACS comes with many analysis tools built-in. A list of all possible possible commands can be obtained by typing {{ic|gmx help commands}}.
GROMACS comes with many analysis tools built-in. A list of all possible possible commands can be obtained by typing {{ic|gmx help commands}}.
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* {{ic|gmx trjconv}} — ''convert and manipulates trajectory files.''
* {{ic|gmx trjconv}} — ''convert and manipulates trajectory files.''
−
==== External libraries & programs ====
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See below for other available tools.
−
Here are a few external analysis tools for writing one's own analysis code or performing calculations not available in the Gromacs package:
+
== See also ==
−
* [
https
://
github
.
com
/
MobleyLab/alchemical-analysis alchemical_analysis
] —
''an open tool implementing some recommended practices
for
analyzing alchemical free energy calculations
.
'' Calls the
[https://
github
.
com
/
choderalab
/
pymbar pymbar
]
package, calculating free energy difference estimates with various methods
.
+
=== Databases ===
−
* [http://
becksteinlab
.
github
.
io
/
GromacsWrapper
/
GromacsWrapper
] —
''a python package that wraps system calls to Gromacs tools into thin classes
.
''
+
* [
http
://
www
.
virtualchemistry.org
/
index.php Virtual Chemistry
] —
comparison of experimental and computational results
for
thousands of molecules
.
Contains validated topology input files for CGenFF, GAFF and OPLS/AA.
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=== Documentation ===
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*
[https://
mailman-1
.
sys.kth.se
/
mailman
/
listinfo/gromacs.org_gmx-users GROMACS Mailing List
]
— very active mailing list for users seeking help. Make sure to read the manual and search the archive before posting
.
+
* [http://
www
.
gromacs
.
org
/
Documentation
/
Manual GROMACS Manual
] —
official GROMACS manual
.
+
+
=== External libraries & programs ===
+
+
==== Analysis libraries ====
* {{AUR|libgmxcpp}} — ''a C++ toolkit used for reading in Gromacs files (.xtc and .ndx) for use in analyzing simulation results.''
* {{AUR|libgmxcpp}} — ''a C++ toolkit used for reading in Gromacs files (.xtc and .ndx) for use in analyzing simulation results.''
* {{AUR|python2-mdanalysis}} — ''an object-oriented python toolkit to analyze molecular dynamics trajectories in many popular formats.''
* {{AUR|python2-mdanalysis}} — ''an object-oriented python toolkit to analyze molecular dynamics trajectories in many popular formats.''
* [http://mdtraj.org/latest/ MDTraj] — ''a modern, open library for the analysis of molecular dynamics trajectories.''
* [http://mdtraj.org/latest/ MDTraj] — ''a modern, open library for the analysis of molecular dynamics trajectories.''
* {{AUR|xdrfile}} — ''allows to read GROMACS trr and xtc files and also to convert from one format to another.''
* {{AUR|xdrfile}} — ''allows to read GROMACS trr and xtc files and also to convert from one format to another.''
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==== Free energy calculations ====
+
* [https://github.com/MobleyLab/alchemical-analysis alchemical_analysis] — ''an open tool implementing some recommended practices for analyzing alchemical free energy calculations.'' Calls the [https://github.com/choderalab/pymbar pymbar] package, calculating free energy difference estimates with various methods.
+
+
==== Topology generation ====
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* [https://code.google.com/p/acpype/ acpype] — ''a tool based on Python to use Antechamber to generate topologies for chemical compounds and to interface with other python applications like CCPN tools or ARIA...Topologies files to be generated so far: CNS/XPLOR, GROMACS, CHARMM and AMBER.''
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+
==== Visualization ====
* {{AUR|vmd}} — '' molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.''
* {{AUR|vmd}} — '' molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.''
−
==
See also
==
+
==
== Wrappers ==
==
−
* [
https
://
mailman-1
.
sys
.
kth.se
/
mailman
/
listinfo/gromacs.org_gmx-users GROMACS Mailing List
] —
very active mailing list for users seeking help. Make sure
to
read the manual and search the archive before posting
.
+
* [
http
://
becksteinlab
.
github
.
io
/
GromacsWrapper
/
GromacsWrapper
] —
''a python package that wraps system calls
to
Gromacs tools into thin classes
.
''
−
* [http://www.gromacs.org/Documentation/Manual GROMACS Manual] — official GROMACS manual.
+
+
=== Tutorials ===
* [http://www.gromacs.org/Documentation/Tutorials GROMACS Tutorials]
* [http://www.gromacs.org/Documentation/Tutorials GROMACS Tutorials]
* [http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html Justin Lemkul's Tutorials] — includes a variety of different simulation methods (umbrella sampling, free energy calculations, etc).
* [http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html Justin Lemkul's Tutorials] — includes a variety of different simulation methods (umbrella sampling, free energy calculations, etc).
* [http://statthermo.blogspot.com/p/tutorials.html James Barnett's Tutorials] — a few basic tutorials on simulations with an organic solute. Includes how to use {{ic|pdb2gmx}} with a user-created molecule.
* [http://statthermo.blogspot.com/p/tutorials.html James Barnett's Tutorials] — a few basic tutorials on simulations with an organic solute. Includes how to use {{ic|pdb2gmx}} with a user-created molecule.