Category:Development

From wiki.gromacs.org

Contents 1 Coding Standards 2 Projects 3 Wish list 4 Developer resources

[edit] Coding Standards

In order to make the GROMACS code more accessible to non-experts we are working on a set of rules for new code, that will successively be implemented for existing code as well.

• Indentation and block structure
• Encapsulation
• Interfaces

[edit] Projects

Here a number of projects are described which we would like volunteers to work on. Since these are new algorithms and extensions to the current code they have to be based on the latest CVS code. If you are interested in helping out, please send email to the gmx-developers mailing list and note your interest on the discussion page for this wiki entry or the special entry for each topic. It is a good idea to thoroughly discuss things with other developers before starting to code. An estimate of the amount of time for each project is given for an experienced C developer. To make the deal somewhat sweeter, some of these projects may be publishable if completed successfully, and one or more of the core developers will probably be interested to make that happen.

A number of "other projects" do not require C-programming, but they do require thorough GROMACS and/or other specialist knowledge.

Item	Target Version	Description	Time Estimate	Status
		CODE RESTRUCTURING
Comments in code	4.1	Restructuring the comments in the code using the http://www.doxygen.org system. Boring but very useful	1 month	TBD
XTC Library	4.1	Fork off the code for reading XDR based files like XTC, EDR, TRR to a separate library, probably to be licensed under a less restrictive license.	1 week	Assigned
Abstract Types	4.x	Change existing structure types to be abstract.	2 weeks	TBD
		MOLECULAR DYNAMICS
Fast multipole	4.x	Implementation of a parallel Fast Multipole solver for computing electrostatic interactions into GROMACS.	6 weeks	TBD
FFTW-3D	4.1	Implementation of 3D decomposition for FFTs (needed for the PME algorithm).	1 month	Assigned
Free Energy Perturbation	4.x	Add the ability to evaluate the energy at a list of alternate lambda values specified in the mdp file every (nstlambda?) steps, where nstlambda or similar is a new flag that specifies how often these should be evaluated. Energies should be dumped to energy file.	?	TBD
Neighborlist-Update	4.0	Dynamically updated neighborlists. Instead of updating every nstlist, regardless of whether there was movement out or in of the cutoff distance, the distance each particle moves can be calculated, and then updating occurs if any particle has moved too far.	< 1 week	Done
Integrator	4.x	Implement better MD integrators than Leap-Frog	1 month	TBD
Monte Carlo	4.x	Implement a Monte Carlo integrator.	1 month	TBD
Docking	4.x	Implement a docking engine	2 months	TBD
Implicit Solvent	4.0	Implement options for implicit solvent simulations.	4 months	Assigned
Barostat	4.x	Implement better functioning Rahman-Parinello barostat	?	TBD
Interactive Molecular Dynamics	4.x	Implement the IMD protocol into Gromacs.	?	Assigned
Position Restraints Development	4.x	Implement new position restraint algorithms	2 weeks	TBD
PME-vdW	4.x	Implement the PME algorithm for long-range vdW interactions	1 month	TBD
		UTILITIES
Edit traj	4.1	Merging trjconv, trjcat and trjorder into one program. The combined program will be rather complicated and it would be good to make the code a whole lot more modular	2 weeks	TBD
Edit box	4.1	Merging genbox, genion, editconf and genconf into one program. The combined program will be rather complicated and usability needs to be improved	2 weeks	TBD
GUI-devel	4.x	Extend/implement (part of) a graphical user interface (GUI) for GROMACS	2-6 months	TBD
		PREPROCESSING
Genvsites	4.x	Write a program that generates virtual sites based on a topology (top) file and writes another topology	4 weeks	Assigned
XML-devel	4.x	Implementation of the XML specification	2 months	Assigned
Topology-Generation	4.x	Extension of the x2top program for different force fields, mainly non-programming chores	1 month	Assigned
Topology-Handling	4.x	Modification of the GROMACS topology/coordinate file handling/atom numbering so that distance/angle/dihedral restraints can be used between "molecules" (in the topology sense); currently they can only be used between atoms within the same "molecule" (although not all components of the "molecule" need to be connected)	?	Assigned
MDP Chaining	4.x	Make it possible to have a few mdp files that are run sequentially on the same topology, e.g. to allow a complete E.M., P.R., M.D. protocol in a single simulation. Obviously this can be scripted as well, but that gives quite a mess of files.	?	TBD
Force-Field Organization	4.0	Organize the force field files in a more logical way using a new directory structure	1 week	TBD
Cpp replacement	4.0	write a small code snippet to replace the C-preprocessor call in grompp	1 week	Done
Extend-tpbconv	4.1	Permit tpbconv to act on multiple files with -extend etc. to suit REMD and multiple MD (this overlaps with Multi I/O below).	2 weeks	TBD
Modularize pdb2gmx	4.1	Divide pdb2gmx into a set of routines that perform the separate functionality.	2 weeks	TBD
		ANALYSIS
Raw matrix data output	4.x	Allow output of raw data from analysis tools, rather than xpm files	1 day	TBD
Support for GNUplot	4.x	Allow output of results to GNUplot rather than xmgrace (or data without formatting at all). This includes checking analysis programs that may write xmgrace style command straight to a file	2 days	TBD
Multi I/O	4.0	Porting the routines that give trjcat and eneconv the possibility to read in many files (e.g. trjcat -f *.xtc -o out.xtc) to all analysis routines	2 weeks	TBD
Analysis-Library	4.x	Modularizing the analysis tools such that one can e.g. compute a radial distribution function for a given set of coordinates. This means separating core of the analysis tools from the main function	1 month	TBD
Analysis Embedding	4.x	Following the previous project: make the analysis library a true callable library for interfacing with scripting languages such as Perl and Python	1 month	TBD
Dynamic Indices	4.x	Replacing index files by make_ndx queries that are executed for each new coordinate set	1 week	TBD
DSSP	4.x	Implement a native DSSP algorithm (secondary structure calculation)	2 weeks	TBD
		OTHER PROJECTS
GUI	4.x	Investigate status of different GUI projects for GROMACS and report to the wiki	2 weeks	TBD
XML-spec	4.0	Development of an XML specification for the description of molecules and input for computer simulations	1-2 months	TBD
Test-set	3.3.2	Development of a more rigorous test set, for mdrun and all other programs	4 weeks	Done
Test-set	4.0	Update the Test Set for 4.0	2 weeks	TBD
Web-maintenance	Any	Clean up the GROMACS website (running under Joomla), plus subsequent maintenance	2 weeks	TBD
Tutorial-writing	Any	Writing new tutorials about different topics, plus subsequent maintenance	1 week	TBD
Wiki-FAQ	Any	Add more FAQs, plus subsequent maintenance	1 week	TBD
Teaching-material	Any	Work on material for teaching MD at different levels of sophistication	weeks to months	TBD

[edit] Wish list

• Two new .mdp options: 1) "nstfrcout" that defines the number of steps between outputting selected forces to a special file = "traj.frc". and 2) "force_grps" that controls output selection to the new file = "traj.frc". Note: This is intended to have no effect on nstfout.

• The ability to make more than one .xtc file with different output selections nstxtcout, xtc_grps, xtc_precision, is desirable for example when one wants to save a small group of selected coordinates every step for processing and the entire coordinates once and a while for later system analysis.

• Seamless integration of AMBER forcefields (http://folding.stanford.edu/ffamber/) into GROMACS.

• Output from all analysis tools also in an human readable style (something like a matrix) and not only in xpm format (http://www.gromacs.org/pipermail/gmx-developers/2004-April/000857.html).

• Adding Canonical sampling through velocity rescaling (G. Bussi, D. Donadio, M. Parrinello J. Chem. Phys. 2007, 126 (1), Art. No. 014101)

• Improved speedup when fixing atoms via freezing and energy_group exclusions. Somehow, when atoms are fixed in place during a CHARMM simulation, the speedup is many times faster than it is in GROMACS. For a comment on how this might be done: http://www.gromacs.org/pipermail/gmx-users/2004-July/011403.html

• Adding -nopbc option to g_dist and g_mindist.

• The ability to read in multiple .ppa files, for example to allow one pull-code implementation of an umbrella in absolute coordinates and one relative to a reference group, or one umbrella and one constraint and one afm, etc.

• Adding "-dt" flag to gmxdump which reports the time step of a trajectory and exits immediately. Very useful!

[edit] Developer resources

• CVS_HowTo With GROMACS-specific info.
• Brief_CVS_Guide by Doug Wright, last update August 29, 1995
• Compiling_CVS GROMACS-specific tips on how to compile the sources once you have downloaded them from CVS
• More_CVS Downloading the manual and the test set
• Development_Tools like autoconf and automake