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Merge branch release-5-1 into release-2016
2016-06-30
Mark Abraham
M
e
rg
e
bra
n
ch relea
s
e-5-1 into release-2016
commit
|
commitdiff
|
tree
2016-06-29
Mark
Abraham
Refactor
s
ysc
o
nf c
h
eck
i
ng
commit
|
commitdiff
|
tree
2016-06-29
Mark A
b
raham
Work around
g
libc 2
.
2
3
w
ith CUDA
commit
|
commitdiff
|
tree
2016-06-28
Mark Abraham
Update to include
a
gc
c
6
.
1 configuration
commit
|
commitdiff
|
tree
2016-06-28
Ma
r
k Abraham
F
i
x SIMD
configu
r
ation management
commit
|
commitdiff
|
tree
2016-06-27
M
a
rk Ab
r
aham
Removed unnecessary
i
nter-simul
a
tion signa
l
ling
commit
|
commitdiff
|
tree
2016-06-27
Mark Abra
h
am
Merge bra
n
ch release-5-1 into release-2016
commit
|
commitdiff
|
tree
2016-06-23
M
ark Abraham
A
l
l
o
w u
s
e of external
lmfit packag
e
commit
|
commitdiff
|
tree
2016-06-23
Mark Abraham
P
r
e
vent use o
f
mdrun
-ma
x
h -multi
commit
|
commitdiff
|
tree
2016-06-22
Mar
k
A
b
raham
Fix configuration-time cpuinfo code
commit
|
commitdiff
|
tree
2016-06-22
Mar
k
Abraham
Me
r
ge branch rele
a
se-5
-
1 int
o
rele
a
s
e
-2
0
16
commit
|
commitdiff
|
tree
2016-06-22
Mark
Abra
h
am
Adjust and docu
m
ent C++11 compiler test
s
commit
|
commitdiff
|
tree
2016-06-20
Mark Abra
h
am
Update pre-submit mat
r
ix co
n
tent
s
commit
|
commitdiff
|
tree
2016-06-19
Ma
r
k
Abraham
Improve docs for lin
k
ing stdlibc++
nee
d
ed by icc
commit
|
commitdiff
|
tree
2016-06-17
Mark Abraham
Merge b
r
anch
release-5-1 into
r
e
lease-2016
commit
|
commitdiff
|
tree
2016-06-17
Mark Abra
h
am
Fi
x
multi
-
sim + DD + simple distance restraints
commit
|
commitdiff
|
tree
2016-06-10
M
ark
Abraham
Find python
f
or d
o
cs bu
i
ld quietly
commit
|
commitdiff
|
tree
2016-06-08
Mark Abra
h
am
M
erge branch release-
5
-1
i
n
t
o
r
elease-2016
commit
|
commitdiff
|
tree
2016-06-07
Mark A
b
raham
Re-a
d
d suppo
r
t for
lin
k
i
ng against external TinyXM
L
-2
commit
|
commitdiff
|
tree
2016-06-07
Ma
r
k Abraham
Upd
a
tes to documen
t
ation
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
F
ix compatibil
i
ty wit
h
older C
M
ake
commit
|
commitdiff
|
tree
2016-06-02
Mark Abra
h
a
m
Mak
e
more
C
Make
v
ariables advanced
commit
|
commitdiff
|
tree
2016-06-02
Mark
A
braham
Ig
n
o
re stderr when detec
t
in
g
SIMD and build info
commit
|
commitdiff
|
tree
2016-05-31
Mark Abraham
Fix referenc
e
to vm
d
i
o
.
c
t
o be vmdio
.
cpp
commit
|
commitdiff
|
tree
2016-05-31
Mark Ab
r
aham
S
econd
2
016 beta r
e
lea
s
e
commit
|
commitdiff
|
tree
2016-05-29
Mark
A
br
a
ham
S
i
mplif
i
ed and updated OpenCL compilation
commit
|
commitdiff
|
tree
2016-05-27
M
ark A
b
raham
Fix
reading of bonded ta
b
l
e
s
commit
|
commitdiff
|
tree
2016-05-26
Mark Abraham
New
q
u
ote
commit
|
commitdiff
|
tree
2016-05-12
Mark Abraham
Merge br
a
nch release
-
5-1 int
o
release-2016
commit
|
commitdiff
|
tree
2016-05-12
Mark Abraham
GRO
M
A
CS 2016 beta1 relea
s
e
commit
|
commitdiff
|
tree
2016-05-10
Mark A
b
raham
Bump clang static analyzer to version 3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Mar
k
Abraham
Minor update to sphi
n
x dependency
commit
|
commitdiff
|
tree
2016-05-10
Mark Abraham
Facilita
t
e lin
k
i
ng with l
i
bcxx
commit
|
commitdiff
|
tree
2016-05-08
Mark Abraham
Fixes for
c
lang 3
.
7 on PowerPC
commit
|
commitdiff
|
tree
2016-05-08
Mark Abraham
Fix cons
t
ant
s
,
u
n
its an
d
c
o
n
v
ersi
o
n factors
commit
|
commitdiff
|
tree
2016-04-27
Mark Abraham
Merge br
a
nch
r
elease-5-1
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Replace libxml2 with tinyxml2 fo
r
use in t
e
s
t code
commit
|
commitdiff
|
tree
2016-04-19
Mark Ab
r
aham
Fix parse_digit
s
_from_strin
g
commit
|
commitdiff
|
tree
2016-04-19
Mark A
b
raha
m
Fix
mdp la
b
e
l
g
enerati
o
n
commit
|
commitdiff
|
tree
2016-04-18
Mark Abraham
R
e
duc
e
c
ompila
t
ion coupling of SIMD m
o
dule
commit
|
commitdiff
|
tree
2016-04-14
Ma
r
k Abraham
M
erge branch
release-5-1
commit
|
commitdiff
|
tree
2016-04-01
Mar
k
Abr
a
ham
Re
v
ert to
t
r
e
atin
g
-1 as "g
e
nerate a se
e
d"
i
n
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
Mark Abraham
Add test
a
nd impro
v
ed docs fo
r
cus
t
om check
S
eque
n
ce
commit
|
commitdiff
|
tree
2016-03-30
M
ar
k
Abraham
Clean
up vsite
c
ode
commit
|
commitdiff
|
tree
2016-03-19
Mark Abrah
a
m
A
d
d more con
s
t
c
orrec
t
ness
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
Fi
x
wa
r
n
i
ng from G
C
C
6
commit
|
commitdiff
|
tree
2016-03-19
M
ark Abraham
Im
p
roved
s
ome
md
r
un integ
r
a
t
ion tests
commit
|
commitdiff
|
tree
2016-03-18
Mark Abrah
a
m
Wa
r
n
about OpenM
P
I
1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Mark A
b
raham
F
i
x
t
y
p
o
i
n
Fourier dihedral equati
o
n
commit
|
commitdiff
|
tree
2016-03-15
Mark
A
br
a
ham
Mer
g
e bra
n
c
h rele
a
se-5-0
into release-
5
-
1
commit
|
commitdiff
|
tree
2016-03-12
M
ark Abraha
m
Updat
e
us
e
of isnan
i
n li
n
earalge
b
ra
commit
|
commitdiff
|
tree
2016-03-12
Mark Abraham
F
i
nd hwloc
q
u
i
etly if it'
s
a
lready been found
commit
|
commitdiff
|
tree
2016-03-11
Mark Abraham
Add infrastruct
u
re for tests t
o
compare mdruns
commit
|
commitdiff
|
tree
2016-03-11
M
a
r
k Abraham
Merge bran
c
h re
l
ease-5-0 i
n
to r
e
le
a
se-5-
1
commit
|
commitdiff
|
tree
2016-03-10
Mark A
b
raham
Require
2
0
1
5 version
for MSVC
commit
|
commitdiff
|
tree
2016-03-05
Mark
Abrah
a
m
Add SETTLE unit tests
commit
|
commitdiff
|
tree
2016-02-26
Mar
k
Ab
r
ah
a
m
Sepa
r
a
t
ed test of CDATA end tag handlin
g
f
rom others
commit
|
commitdiff
|
tree
2016-02-23
Mark Abraham
Replace cppch
e
ck
s
u
ppression in
checkpoint co
d
e
commit
|
commitdiff
|
tree
2016-02-22
M
ark Abraham
Move
in
i
t
of speciali
z
ed
d
ynami
c
al
a
lgorithms to
d
o
_md
commit
|
commitdiff
|
tree
2016-02-21
Mark Abra
h
am
Separa
t
e table constr
u
ct
i
o
n
commit
|
commitdiff
|
tree
2016-02-19
Mar
k
Abraham
Merg
e
branch rele
a
se-5-1
commit
|
commitdiff
|
tree
2016-02-19
Mark
Abr
a
ham
M
a
ke both
f
t
p and http lin
k
s
f
or source download
commit
|
commitdiff
|
tree
2016-02-18
Mark Abraham
Updated
r
efe
r
ence
m
anual text about
PME tuning
commit
|
commitdiff
|
tree
2016-02-16
Mark Abraham
Merge branch release-5-0 into
r
elease-
5
-1
commit
|
commitdiff
|
tree
2016-02-14
M
ark Abraham
Re
-
gen
e
r
ated eps
f
or
figu
r
e 4
.
8
commit
|
commitdiff
|
tree
2016-02-10
Mark Abraham
Re-remove *_stoc
h
d_state function declara
t
io
n
s
commit
|
commitdiff
|
tree
2016-02-10
Mark Ab
r
aham
I
mproved update_coords handlin
g
of x
p
ri
m
e
commit
|
commitdiff
|
tree
2016-02-10
Mark Ab
r
aham
Fix iss
u
es
t
o
u
pda
t
e c
p
pcheck support t
o
1
.
72
commit
|
commitdiff
|
tree
2016-02-08
M
a
r
k
Abraham
Merge bran
c
h r
e
leas
e
-5-
0
i
nto rele
a
se-
5
-1
commit
|
commitdiff
|
tree
2016-02-06
Mark
Abr
a
ham
M
e
rge branch releas
e
-
5
-1
commit
|
commitdiff
|
tree
2016-02-03
M
ark Abraha
m
B
umped pat
c
h nu
m
b
e
r to prepare for future
5
.
1
.
3 release
commit
|
commitdiff
|
tree
2016-02-03
Mark
A
braham
Version
5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
M
a
rk
A
b
r
a
ham
F
ix grompp no
t
w
a
r
ning wh
e
n
.
mdp values have wr
o
ng
.
.
.
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
M
erge r
e
leas
e
-
5
-
0
into rel
e
ase-5-1
commit
|
commitdiff
|
tree
2016-02-03
Mark
Abraham
Fix dEkin/dl handli
n
g
w
ith
multiple ran
k
s
commit
|
commitdiff
|
tree
2016-01-28
Mark
Ab
r
aham
Merge
branch
r
e
lease-5-1
commit
|
commitdiff
|
tree
2016-01-28
Mark
Abraham
F
i
x
use of __APPLE__ in
O
penCL code
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Add
OpenCL s
o
u
r
c
e
fi
l
e ty
p
es
to copyrig
h
t checker
commit
|
commitdiff
|
tree
2016-01-28
Mar
k
Ab
r
a
h
a
m
Avoid FP exception
commit
|
commitdiff
|
tree
2016-01-27
Mark Abraham
M
erge branch release-5-1
commit
|
commitdiff
|
tree
2016-01-27
Mark Ab
r
aham
Remov
e
b
NotL
a
stFrame
commit
|
commitdiff
|
tree
2016-01-27
Mark Abraham
Add
s
uggestions f
o
r upd
a
ting
b
i
nut
i
ls
commit
|
commitdiff
|
tree
2016-01-26
Mark Abraham
Fix defa
u
lt for GMX_
U
S
E
_N
V
ML
commit
|
commitdiff
|
tree
2016-01-25
M
a
rk Ab
r
aha
m
M
erge branch re
l
ease-5-1
commit
|
commitdiff
|
tree
2016-01-24
Mark Abraham
Fix
duplicat
e
LaTeX equa
t
i
on label
commit
|
commitdiff
|
tree
2016-01-24
Mark Abraham
Update ref
e
rences
t
o HT
M
L
and online doc
u
m
e
ntation
commit
|
commitdiff
|
tree
2016-01-14
Mark Abraham
Permit customized testing
o
f
grompp and mdrun
commit
|
commitdiff
|
tree
2016-01-13
M
a
rk Abraham
Allo
w
ed NVML
s
uppor
t
t
o
be toggle
d
commit
|
commitdiff
|
tree
2016-01-12
Mark
Abraham
Me
r
ge bra
n
ch release
-
5-0 int
o
r
e
lease-5-1
commit
|
commitdiff
|
tree
2016-01-11
Mark Abraham
Improved
u
p
date_coo
r
ds
commit
|
commitdiff
|
tree
2016-01-08
Mark Abraham
Impro
v
e
tpr he
a
der ver
s
ion handl
i
ng
commit
|
commitdiff
|
tree
2016-01-08
Mark Abraham
M
e
rge
b
r
a
nch re
l
ease-5-
1
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
F
i
x some md
r
un header
depend
e
ncies
commit
|
commitdiff
|
tree
2016-01-07
Mark Ab
r
a
ham
A
void more C++ bindings for M
P
I
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Doc
u
ment how po
t
ential-sw
i
tch works
commit
|
commitdiff
|
tree
2016-01-07
M
a
r
k
Abraham
Sto
p
usin
g
UNDEFINED as n
a
m
e
of a symbo
l
commit
|
commitdiff
|
tree
2016-01-07
Mark A
b
ra
h
a
m
Remove fields us
e
d
o
n
ly for SD
2
commit
|
commitdiff
|
tree
2016-01-07
Mark
A
braham
B
ackport md-vv fixes
commit
|
commitdiff
|
tree
2016-01-07
Mar
k
Abra
h
am
Remove
SD2
i
ntegrator
commit
|
commitdiff
|
tree
2016-01-06
Mark Abraham
Fix spur
i
o
us g
c
c warning
commit
|
commitdiff
|
tree
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