On Fri, Nov 11, 2011, Yong Duan wrote:
>
> Here is a set of sample files related to ff11pol. This is not the final
> version, meant for checking the code and format only.
I've checked these in to the ff11 branch, and propose that development of
ff11pol (along with ff11 fixed charge models) initially take place in this
branch. I've merged all of master (except Yong's last re-revert) into
ff11, so for right now, the diffs between ff11 and master look correct:
-----------------------------------------------------------------------------
poincare% git diff --stat master
AmberTools/src/leap/src/leap/amber.c | 329 +-
AmberTools/src/leap/src/leap/atom.c | 9 +-
AmberTools/src/leap/src/leap/atom.h | 1 +
AmberTools/src/leap/src/leap/basics.c | 6 +
AmberTools/src/leap/src/leap/build.c | 19 +-
AmberTools/src/leap/src/leap/cmap.h | 28 +
AmberTools/src/leap/src/leap/commands.c | 166 +-
AmberTools/src/leap/src/leap/defaults.h | 6 +
AmberTools/src/leap/src/leap/helptext.text | 61 +-
AmberTools/src/leap/src/leap/model.c | 41 +-
AmberTools/src/leap/src/leap/parmSet.c | 117 +-
AmberTools/src/leap/src/leap/parmSet.h | 35 +-
AmberTools/src/leap/src/leap/tools.c | 6 +-
AmberTools/src/leap/src/leap/unitio.c | 522 ++-
AmberTools/src/leap/src/leap/xaAtomParmTable.c | 6 +-
AmberTools/src/leap/src/leap/xaImproperParmTable.c | 64 +-
AmberTools/src/leap/src/leap/xaTorsionParmTable.c | 71 +-
dat/leap/cmd/leaprc.ff11pol | 188 +
dat/leap/cmd/leaprc.ff11r4 | 192 +
dat/leap/cmd/leaprc.ff11r6 | 192 +
dat/leap/lib/all_amino11.lib | 3447 ++++++++++++
dat/leap/lib/all_amino11basic.lib | 3447 ++++++++++++
dat/leap/lib/all_amino11pol.lib | 3521 ++++++++++++
dat/leap/lib/all_aminoct11.lib | 3215 +++++++++++
dat/leap/lib/all_aminoct11basic.lib | 3215 +++++++++++
dat/leap/lib/all_aminoct11pol.lib | 3677 +++++++++++++
dat/leap/lib/all_aminont11.lib | 3303 ++++++++++++
dat/leap/lib/all_aminont11basic.lib | 3303 ++++++++++++
dat/leap/lib/all_aminont11pol.lib | 3839 +++++++++++++
dat/leap/lib/all_nucleic11.lib | 7129 +++++++++++++++++++++++++
dat/leap/parm/frcmod.ff11 | 342 ++
dat/leap/parm/frcmod.ff11pol | 180 +
dat/leap/parm/frcmod.ff11r4 | 286 +
dat/leap/parm/frcmod.ff11r6 | 344 ++
dat/leap/parm/parm11.dat | 1184 ++++
dat/leap/parm/parm11pol.dat | 756 +++
doc/ff11.html | 95 +
doc/objectiveFn.png | Bin 0 -> 9966 bytes
23 files changed, 41855 insertions(+), 4 deletions(-)
-----------------------------------------------------------------------------
If we are lucky, both the leap code and the data files now in ff11 are in
sync. I'll try next to add in Yong's examples to make some test cases
working; ff11pol developers are of course in the best position to do this, and
that is encouraged.
....dac
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Received on Sat Nov 12 2011 - 08:00:03 PST
