Gromacs units are hard-codes for the Boltzmann inversion of potentials.

$ ~/votca/src/csg/src/tools/csg_map --no-map --top topol.tpr --trj conf.gro  --out conf2.gro

(from trac)

-open a pipe to gnuplot
-allow plotting of table and distributions

if [[ ${TRAVIS_BRANCH} = future ]]; then
  git submodule forearch git checkout master
  git submodule forearch git pull
fi

Many member variables are not initialized, e.g. Bead userdata

Now type1, type2 are glob matched (only ?*) against the type in topology.

Add advanced type selection by:
-name
-index group (reading of these file types is not implemented yet)
-advanced stuff by python functions

add pressure correction update scheme for relative entropy based 
coarse-graining similar to that in IBI. Model CG interactions as B-spline + 
A(1-r/rcut) and update B-Spline knots with RE and A from pressure correction 
update formula. Store both B-spline knots and A at each iteration.

Adding an nrexcl like option to the mapping file would be nice to avoid the 
need to create phantom bonds to model the same exclusions as gromacs.

Also see issue votca/csg#161 for details.

-will be needed for analysis within espresso++
-useful to write quickly little analysis tools

All pbc algorithms have special conditions which are not checked currently. 
This should be done in setBox, make this function virutal which also allows to 
initialize other variables for the pbc algorithm which might be required in 
future.

csg_dump settings file generation
(something like: generate option --setting)

Force matching of a large trajectory can take several hours.
Using threads would be very useful.

Bonded and non-bonded interactions have no uniform interface in c++. This would 
be good to have to allow for easier implementation of e.g. many body 
interactions and more, especially for force-matching.

A concept similar to espresso++ would be nice.

Gromacs does it as well

http://redmine.gromacs.org/issues/685

git clone --recursive [email protected]:votca/votca
mv ~/${TRAVIS_REPO_SLUG} votca

(from trac)

when writing out files for histograms, potential tables or value lists, it 
would be nice to have a comment line in the beginning, that describes, which 
data have been used actually.

For example in a value file:

votca/csg#1:BAB-angle:2 (containing beads B2 A3 B3), 1:ABAB-dihedral:2 (containing 
beads A2 B2 A3 B3)

It seems like bonded distributions are not normalized correctly for bonded 
interactions.

For IBI that doesn't matter too much, but we should at least normalize them 
with bin size and count.

-add a section to the manual
-naming scheme

table format should be:
x y ... flag
(flag in last column)

Check if csg_boltzmann used this format

Dominik said potential.do and pressure.do are very unclear in the manual. We 
need to add an example and improve the doc (also in the xml file)

The two functions FirstFrame and NextFrame in many casees is very unhandy to 
use in code. A single ReadFrame function would be more convenient.

Currently short CG MD simulation is performed in each relative entropy update 
step to compute CG ensemble averages. Alternative approach is to reweight the 
initial (step 0) CG configurations to obtain CG ensemble averages (Eq. 54 
Chaimovich and Shell, J. Chem. Phys. 134, 094112, 2011). 
This eliminates the need to perform CG-MD in each RE update and hence, reduces 
the computation time.

- number density
- improved atom selection capabilities

Using index numbers, ids or pointers is not done consistently. Access by index 
should be avoided whenever possible since it can lead to serious problems when 
e.g. changing number of particles or reordering them.

DCD trajectory support is needed for native NAMD support. Unfortunately, DCD is 
a very complicated format.

I guess the easiest would be to copy vmd* from the gromacs sources and change 
the functions in vmdio.c to a VOTCA trajectory reader.

The VMD files are under BSD license so that should not be a problem.

As a bonus we get all other formats supported by VMD for free.