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Merge "Merge release-4-5-patches into release-4-6" into release-4-6
2012-03-15
Mark Abraham
C
lar
i
fied
wordin
g
of
d
ocumentat
i
on
commit
|
commitdiff
|
tree
2012-03-14
Mark
A
braham
C
han
g
e
d cryptic erro
r
mes
s
a
g
es
a
bout disk quo
t
a
commit
|
commitdiff
|
tree
2012-03-09
Ma
r
k Abraham
More ed
i
to
r
ial fixes
t
o tool docu
m
entation
commit
|
commitdiff
|
tree
2012-03-09
Mark
A
braham
Editorial chang
e
s to
too
l
s documentatio
n
commit
|
commitdiff
|
tree
2012-03-08
Mark Abrah
a
m
Impr
o
ved warning
n
o
te with
D
D
and pe
r
i
o
dic m
o
lecules
commit
|
commitdiff
|
tree
2012-03-08
Mark Abr
a
ham
M
ade
d
escriptio
n
st
r
ing for g_s
e
l
ec
t
-select clearer
commit
|
commitdiff
|
tree
2012-03-08
Mark Abr
a
ham
Imp
r
oved cryptic erro
r
message
commit
|
commitdiff
|
tree
2012-02-24
Mark
A
braham
Minor f
o
rmatting fixes to
.
mdp
o
ption docu
m
enta
t
i
on
commit
|
commitdiff
|
tree
2012-02-23
M
a
rk Ab
r
aham
Fix
p
db2gm
x
-
cmap in cor
n
er cases
commit
|
commitdiff
|
tree
2012-02-10
Mark Abrah
a
m
Fixed g_
s
ham using
more than th
r
ee
dimens
i
ons
commit
|
commitdiff
|
tree
2012-02-10
Mark Abr
a
h
am
Integer
m
ultipl
i
catio
n
that checks for ov
e
rflow
commit
|
commitdiff
|
tree
2012-02-01
Mark Ab
r
aham
Fixed tr
j
co
n
v
-sub
commit
|
commitdiff
|
tree
2012-02-01
Mar
k
Abraham
Fixe
d
error m
e
ssage
t
o
identify the correct file
commit
|
commitdiff
|
tree
2012-02-01
Mark Abr
a
h
am
Improved erro
r
messag
e
commit
|
commitdiff
|
tree
2012-01-31
Mark Abrah
a
m
Merge "
C
orrec
t
e
d
use of ?:
i
n condi
t
iona
l
" into release
.
.
.
commit
|
commitdiff
|
tree
2012-01-31
Mar
k
Abraham
Mad
e
error message
e
v
e
n more explici
t
commit
|
commitdiff
|
tree
2012-01-31
Mar
k
Abraham
Co
r
re
c
ted use of
?: in con
d
itional
commit
|
commitdiff
|
tree
2012-01-14
Mar
k
Abraham
Merge "Rem
o
ve use of F
i
ndMPI
.
cmake" into rele
a
se-
4
-6
commit
|
commitdiff
|
tree
2012-01-14
Mark Ab
r
aham
Me
r
ge "Removing
o
u
tdated vsite comment" into release-4-6
commit
|
commitdiff
|
tree
2012-01-14
Mark Abraham
Remove u
s
e of
Fi
n
dMPI
.
cmake
commit
|
commitdiff
|
tree
2012-01-10
Mark A
b
raham
Fixed use o
f
isfinite and _isfinite
commit
|
commitdiff
|
tree
2012-01-09
Mark Abraham
Fixed MSVC comp
i
l
i
ng
w
ith plug-in sup
p
ort
commit
|
commitdiff
|
tree
2012-01-09
Ma
r
k Abraham
Fixed use of _snprintf_s with MSVC
commit
|
commitdiff
|
tree
2012-01-07
Ma
r
k Abr
a
ha
m
Made use of VMD plugin
s
more robust
commit
|
commitdiff
|
tree
2012-01-04
Mark Abraham
Added CMake Toolchain file for
B
lueGene/P
commit
|
commitdiff
|
tree
2011-12-29
Mar
k
Abraham
Documented
t
he function o
f
g_clust
e
r -cl -noav
commit
|
commitdiff
|
tree
2011-12-14
Mark Abraham
Re-fi
x
ed static linking of
m
aths
l
ibraries
unde
r
UNIX
commit
|
commitdiff
|
tree
2011-12-13
Mark Abraham
C
o
n
v
e
rted
macro usag
e
f
or readab
i
lity
commit
|
commitdiff
|
tree
2011-12-13
Ma
r
k
Abraham
Relaxed some
a
ssumptions
ab
o
ut
t
rajectory
t
i
me
s
commit
|
commitdiff
|
tree
2011-12-12
Mark Abra
h
a
m
Fixed mac
r
os that
en
d
e
d
in sem
i
colons
commit
|
commitdiff
|
tree
2011-11-25
Mark A
b
raham
Changed cr
y
ptic
variabl
e
names
commit
|
commitdiff
|
tree
2011-11-24
M
a
rk Abraham
Only analyse an
g
le transitions for dihedral an
g
les
commit
|
commitdiff
|
tree
2011-11-24
Mark Abraham
Added p
r
o
te
c
t
ive p
r
eprocessor directives
commit
|
commitdiff
|
tree
2011-11-23
Mark Ab
r
aham
Fixed
g_angle -
f
-
or to c
o
py times from -f to -or
commit
|
commitdiff
|
tree
2011-11-02
Mark Abr
a
ham
Fix for GB, d
o
uble, SSE2 and optimized ke
r
nels
commit
|
commitdiff
|
tree
2011-11-01
Mar
k
Abraha
m
Tri
g
g
er
c
orrect kern
e
ls under Cygwi
n
commit
|
commitdiff
|
tree
2011-10-27
Mark Abrah
a
m
Made reading of binary matric
e
s
m
ore robust
commit
|
commitdiff
|
tree
2011-10-19
Mar
k
Abraha
m
C
o
r
rected char
g
e
of C
H
ARMM zinc ion to
+
2
commit
|
commitdiff
|
tree
2011-10-13
Ma
r
k A
b
raham
Changed de
f
au
l
t
value
for g_anaeig -
l
as
t
t
o
-1
commit
|
commitdiff
|
tree
2011-10-06
M
ark
Abr
a
ham
Removed erroneous use of MASSV on
B
lueGene
commit
|
commitdiff
|
tree
2011-10-06
Mark Abraham
Fixes
for GB ker
n
el
commit
|
commitdiff
|
tree
2011-09-30
Mar
k
Abraham
Re
m
oved dupl
i
c
ate CMake function
a
lity
commit
|
commitdiff
|
tree
2011-09-27
Mark Abraham
Add
e
d tip for converting
.
xp
m
to someth
i
ng useful
commit
|
commitdiff
|
tree
2011-09-27
Mark Abraham
R
e
mov
e
d
autotoo
l
s and references to t
h
em
.
commit
|
commitdiff
|
tree
2011-09-26
Mar
k
Abraham
Dropped some h
i
nt
s
in the
d
ocumentat
i
on
commit
|
commitdiff
|
tree
2011-09-26
Mark
Abr
a
ham
Removed CMa
k
e
w
arning
for
r
ece
n
t
OpenM
P
I versi
o
ns
commit
|
commitdiff
|
tree
2011-09-23
Mark
Abra
h
a
m
Minor ho
u
se-
k
eeping
commit
|
commitdiff
|
tree
2011-09-15
M
ark Abraham
Fix trj
c
onv -s
u
b
commit
|
commitdiff
|
tree
2011-09-15
Mark Abraha
m
Warning about
trjc
o
nv
-sub needi
n
g
many files open
commit
|
commitdiff
|
tree
2011-09-15
Mark Abraham
g_s
h
am -m
d
ata is an in
p
ut
f
ile
,
not output file
commit
|
commitdiff
|
tree
2011-09-14
Mark Abraham
F
o
r
mat wa
r
n
ing better
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
F
ix pdb
2
gmx
-debug and
.
hdb files
commit
|
commitdiff
|
tree
2011-09-13
Mark Abraham
Fix for C
M
a
k
e
finding LA
P
ACK
commit
|
commitdiff
|
tree
2011-09-13
Ma
r
k Abraham
A
d
ded ACE a
n
d
C
T
3
to
CHAR
M
M27 ami
n
oacids
.
rtp
commit
|
commitdiff
|
tree
2011-09-13
M
ark Abraham
Fixed charge groups of CHARMM27 DNA
/
RN
A
termina
l
H
commit
|
commitdiff
|
tree
2011-09-13
Mark Ab
r
aham
Fixes f
o
r
C
Ma
k
e
fin
d
i
n
g FORT
R
AN l
i
b
rary n
a
mes on POWER6
commit
|
commitdiff
|
tree
2011-09-06
Mark A
b
ra
h
a
m
Fix bug wi
t
h la
r
ge
i
n
t
s
w
itho
u
t
MPI_
I
N_PLAC
E
commit
|
commitdiff
|
tree
2011-09-01
M
ar
k
Abraham
M
ade grompp note abou
t
non-zero charge more useful
commit
|
commitdiff
|
tree
2011-09-01
Ma
r
k Abr
a
ham
Re-implemented g
e
nerati
n
g default
p
r
otein i
n
d
e
x
groups
commit
|
commitdiff
|
tree
2011-09-01
Mark Abr
a
h
a
m
Adjusted construction
o
f
default i
n
d
ex
g
rou
p
s
commit
|
commitdiff
|
tree
2011-09-01
Mark
Abraham
Fixed comment
commit
|
commitdiff
|
tree
2011-08-23
Mark Abraham
Fixed
g
_d
i
sre derefe
r
encing cr
commit
|
commitdiff
|
tree
2011-08-23
Mark
A
b
raham
Typo fix
commit
|
commitdiff
|
tree
2011-08-19
M
a
rk Abraham
Expla
i
ned terminal
residues
a
nd AMBER
in pd
b
2gmx -h
commit
|
commitdiff
|
tree
2011-08-16
M
a
r
k Abraha
m
Made free e
n
ergy pe
r
turba
t
ion work with CMAP
commit
|
commitdiff
|
tree
2011-08-03
Mark Ab
r
aha
m
Fixed outp
u
t
b
ug in demu
x
.
pl
commit
|
commitdiff
|
tree
2011-07-17
Mark Abrah
a
m
Streamlined small par
t
of pdb
2
gmx
commit
|
commitdiff
|
tree
2011-07-15
Mark Abraham
R
eading a
.
g96
tr
a
jectory now causes fatal erro
r
commit
|
commitdiff
|
tree
2011-07-11
Mark
A
br
a
ham
F
ix som
e
i
d
en
t
ifier
n
am
i
ng issues in
l
ast
commit
commit
|
commitdiff
|
tree
2011-07-11
Mark Abraham
Avoided some integer o
v
erflows
commit
|
commitdiff
|
tree
2011-07-08
Mark Ab
r
aham
Cla
r
ified use of OPLS
/
AA zwitterion termini
commit
|
commitdiff
|
tree
2011-07-08
Mark Abraham
Fixed
i
mproper file cl
o
se with GB and mdrun -de
b
ug
commit
|
commitdiff
|
tree
2011-07-08
Mark Ab
r
a
ham
Made pdb2gmx
e
rr
o
r message les
s
c
r
y
ptic
commit
|
commitdiff
|
tree
2011-06-29
M
a
rk Abraham
R
e
vert "draft"
commit
|
commitdiff
|
tree
2011-06-29
Mark
Abraham
Im
p
roved
e
rror messa
g
e an
d
docu
m
entatio
n
commit
|
commitdiff
|
tree
2011-06-29
Mark Abraham
d
r
aft
commit
|
commitdiff
|
tree
2011-06-21
Mar
k
Abraham
E
x
panded LINCS warning text
commit
|
commitdiff
|
tree
2011-06-07
Mark Abraham
Fixed spelling
o
f rep
r
oducible
commit
|
commitdiff
|
tree
2011-05-11
Mark A
b
raham
Added reference to g_s
a
s
-
h
commit
|
commitdiff
|
tree
2011-05-11
Mark Abraham
Cleaned up
g
_sa
s
help text
commit
|
commitdiff
|
tree
2011-05-09
M
ar
k
Abrah
a
m
Added
hint
a
b
o
ut call
i
ng t
r
jconv more than on
c
e
commit
|
commitdiff
|
tree
2011-05-09
Ma
r
k Abraham
Spaced
o
ut par
a
gr
a
phs in trjconv help
commit
|
commitdiff
|
tree
2011-05-02
Mark Abra
h
am
R
emoved
duplic
a
t
e definition of md_print_warning
(
)
commit
|
commitdiff
|
tree
2011-05-01
Mark Abra
h
am
Fi
x
ed d
e
scr
i
ption of
.
m
d
p option to "h-bond
s
"
commit
|
commitdiff
|
tree
2011-04-14
Mar
k
Ab
r
aha
m
R
emoved unnecessary
#
includes
commit
|
commitdiff
|
tree
2011-04-14
Mark Abrah
a
m
Dele
t
ed duplicated code
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
M
oved various
supp
o
r
t
func
t
ions for do_md i
n
to m
d
l
i
b
commit
|
commitdiff
|
tree
2011-04-14
Ma
r
k Abraham
Moved
itera
t
ed
-
cons
t
raints code
i
nto
md
l
ib
commit
|
commitdiff
|
tree
2011-04-14
M
a
rk Abraham
Moved
heuristic neighbo
r
-lis
t
code into mdlib
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Fixed
c
o
de duplicat
i
on
commit
|
commitdiff
|
tree
2011-04-14
Mark Abraham
Fi
x
ed head
e
r #if
n
def test
commit
|
commitdiff
|
tree
2011-03-30
Mark
Abra
h
am
Removed useles
s
const qualifier
commit
|
commitdiff
|
tree
2011-03-30
Mark Abraham
Sup
p
ressed Cygwin C-only compi
l
er warnings
commit
|
commitdiff
|
tree
2011-03-26
Mark Abra
h
am
Fixed g_cl
u
ster logic error
commit
|
commitdiff
|
tree
2011-03-26
M
a
rk Abraham
M
a
de gmx_rmpb
c
_t obje
c
t functions not segfa
u
lt
commit
|
commitdiff
|
tree
2011-03-26
Mark
A
braha
m
F
i
xed matio
.
c sfre
e
() that made DvdS cry
.
commit
|
commitdiff
|
tree
2011-03-08
Mark Abra
h
a
m
Added grompp note a
b
out avoiding
zero
-
step EM
commit
|
commitdiff
|
tree
2011-02-16
Mark Abraham
Cla
r
ified
s
ource
o
f
g_rmsf reference
frame
commit
|
commitdiff
|
tree
2011-02-13
Ma
r
k
Ab
r
aham
Added wo
r
karound for
F_GB13
d
uplicates
commit
|
commitdiff
|
tree
2011-02-13
Mark Abraham
F
i
x
e
d erroneous floating-po
i
nt
c
o
m
parison
commit
|
commitdiff
|
tree
next