To Do

Fix double precision -- Irek

Best practice were used only for qdyn5 files and only with kind prec. There are still some real, and real(4) which should be changed for appropriate precision.

Files used for qdyn5:

exc.f90

index.f90

mask.f90

maskmanip.f90

md.f90

misc.f90

mpiglob.f90

nrgy.f90

parse.f90

prmfile.f90 - precision not fixed

qatom.f90 - line 1993 not added _prec flag

qdyn.f90

sizes.f90

topo.f90

trj.f90

In the program there are some reals initialized by integers it should be corrected.

Constants -- Irek

Move constants to one file. These are spread all over the code.

Fix discrepancy results -- Irek

Without ifort flags -fp-model precise and -fp-model except program gave different results depend on architecture. Need to be fix those flags are slowing speed of program.

UML Diagram -- Masoud and Mauricio

A UML diagram is needed to get a better fast idea of how the code is organized and who calls what.

Add more Tests -- Mauricio

• water sphere alone -- radial distribution functions
• water sphere plus ions -- solvation free energy
• alanine dipeptide and tripeptide -- for conformational check in Phi/Psi space
• n-butane (FEP)
• 2,4-quinazolinediamine -- also conformational?

Tests for speed -- Miha

DHFR.

A stale branch with a clean version of the MPI implementation by Ake Sandgren can be found at:

https://github.com/qusers/qsource/tree/testing/akesandgren

This might be useful for benchmarking as a standard.

Implement BAR (Bennet's Acceptance Ratio) -- Unassigned

Johan Sund did it. Have to rescue the code.