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Fixed TNG memory alignment problem and reset pointers.
2014-08-21
Magnus Lundb
o
r
g
Fixe
d
T
N
G m
e
mor
y
alignm
e
nt problem and reset po
i
nters
.
commit
|
commitdiff
|
tree
2014-08-20
Erik L
i
ndahl
Add _GN
U
_SOURC
E
=1 to fin
d
clone()
w
ith PGI
commit
|
commitdiff
|
tree
2014-08-20
Ro
l
an
d
Schulz
Change er
r
o
r to warning for m
i
ssing OMP
_
NUM_THREADS
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
Fix matrix pointer derefere
n
ce
bug
in update
.
c
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
E
n
abl
e
SIM
D
re
g
ister c
a
lling convention
with
g
mx_s
i
m
d
call
commit
|
commitdiff
|
tree
2014-08-20
Erik Lind
a
hl
Add
c
y
cle counters for 64-b
i
t A
R
M
commit
|
commitdiff
|
tree
2014-08-20
Erik
L
inda
h
l
Sho
r
ten
p
lugin co
n
fi
g
uration message
commit
|
commitdiff
|
tree
2014-08-17
Eri
k
L
i
ndahl
Fix Por
t
l
a
n
d c
o
mpiler warning
s
commit
|
commitdiff
|
tree
2014-08-17
B
e
rk Hess
Halved
the c
o
st of the pul
l
comm
u
ni
c
a
tion
commit
|
commitdiff
|
tree
2014-08-17
Roland Schulz
Do
n
't build t
e
s
t
s
u
ntil
t
hey
a
re
r
un
commit
|
commitdiff
|
tree
2014-08-16
Mark
Abraham
Fix gmx
tune_p
m
e with LJ-PME
commit
|
commitdiff
|
tree
2014-08-16
Mark Abr
a
ham
Fix wallcycle co
u
nting with m
d
-vv, sd and sd2
commit
|
commitdiff
|
tree
2014-08-16
Teemu Murtola
Disable a
n
a
l
ysisdata gen
e
r
ic tests if not compilab
l
e
commit
|
commitdiff
|
tree
2014-08-14
Berk
Hess
Co
r
rect
e
d
S
IM
D
math overflow do
c
umentation
commit
|
commitdiff
|
tree
2014-08-10
Eri
k
Lin
d
a
hl
Impr
o
ve G
r
oma
c
s po
r
tability
commit
|
commitdiff
|
tree
2014-08-10
Erik
L
i
n
dahl
Rep
l
ace __LP64__ with check f
o
r pointer
s
ize
commit
|
commitdiff
|
tree
2014-08-10
Berk
H
e
ss
Added checks for TPI
+
Verlet scheme
commit
|
commitdiff
|
tree
2014-08-10
R
o
land Schu
l
z
Check MD5su
m
f
or regressiontest
commit
|
commitdiff
|
tree
2014-08-07
Er
i
k Lin
d
ahl
Fix
p
o
rtability i
s
sue w
i
th ArrayRef initialize
r
ov
e
rloading
commit
|
commitdiff
|
tree
2014-08-07
Erik Lindahl
Changed names of te
s
t
files to avoid F
u
jitsu compi
l
er bug
commit
|
commitdiff
|
tree
2014-08-05
Ber
k
Hess
Fi
x
ha
n
g
with LJ-PME and empty domains
commit
|
commitdiff
|
tree
2014-08-05
Ro
l
and Schulz
W
o
rkaround for ICC 14
commit
|
commitdiff
|
tree
2014-08-01
Erik Lindahl
Added tests for denorm
a
l and un
d
e
r
flow for simd
e
xp()
commit
|
commitdiff
|
tree
2014-07-28
R
oland Schulz
F
ix build
of binary package
commit
|
commitdiff
|
tree
2014-07-28
Roland Sch
u
lz
R
e
mo
v
e Random123/features
commit
|
commitdiff
|
tree
2014-07-25
Roland Schulz
Wor
k
around for ICC 14
bu
g
commit
|
commitdiff
|
tree
2014-07-24
Rola
n
d S
c
hul
z
F
i
x Cygw
i
n+Share
d
-Li
b
s+FF
T
W
commit
|
commitdiff
|
tree
2014-07-21
Roland Schulz
Fix GMX_
N
ONBONDED_NUM_THR
E
ADS
!
=GMX_P
A
IRSEARCH_NUM_
T
HREADS
commit
|
commitdiff
|
tree
2014-07-16
Teemu Murt
o
la
Fix
HTML
h
elp and man pages
for comm
a
nds
w
ith dashes
commit
|
commitdiff
|
tree
2014-07-13
E
rik Linda
h
l
Avoid clang/32 optimizati
o
n
a
f
fecti
n
g
I
E
E
E
endian
detection
commit
|
commitdiff
|
tree
2014-07-11
Teemu
Murt
o
l
a
Fix
H
TM
L
l
inks that co
n
tain
file extensions
commit
|
commitdiff
|
tree
2014-07-09
M
a
rk Abraham
Quieten repeated cmake
runs
commit
|
commitdiff
|
tree
2014-07-09
Roland Schulz
Fix Cygwin
b
uild
commit
|
commitdiff
|
tree
2014-07-08
Erik L
i
ndahl
Make
IEEE754 check mo
r
e
robust
commit
|
commitdiff
|
tree
2014-07-08
Tee
m
u Mur
t
o
la
Make selec
t
io
n
s ignore \r
i
n input
commit
|
commitdiff
|
tree
2014-07-07
Mark
A
b
raham
Fix tarba
l
l and ins
t
all, particularly for INSTALL
commit
|
commitdiff
|
tree
2014-07-05
M
a
gnus L
u
ndbor
g
Fix bug
c
a
u
sing reading n
e
xt f
r
a
m
e not to stop
.
commit
|
commitdiff
|
tree
2014-07-05
M
a
gnus Lu
n
d
b
or
g
Fix tng_num_fr
a
me_
s
ets_g
e
t() w
i
th no
frame sets
.
commit
|
commitdiff
|
tree
2014-07-05
Teemu Mur
t
ola
R
e
i
n
stant
i
at
e
unsort
e
d inde
x
grou
p
chec
k
commit
|
commitdiff
|
tree
2014-07-05
Roland Schulz
Add running tests
to
i
nsta
l
l-guide
commit
|
commitdiff
|
tree
2014-07-05
Te
e
mu Murtola
Update s
o
me ins
t
al
l
ation-rela
t
ed docs
commit
|
commitdiff
|
tree
2014-07-01
Mark Abr
a
h
am
Fix
G
Mock
t
o work on MSVC
commit
|
commitdiff
|
tree
2014-06-29
Mark Abra
h
am
Refer to "mix
e
d" pr
e
c
isio
n
in user-faci
n
g do
c
ument
a
ti
o
n
commit
|
commitdiff
|
tree
2014-06-29
B
e
rk Hess
Take LJ-PME
i
nto account
f
or table spacing
commit
|
commitdiff
|
tree
2014-06-29
Erik Lin
d
ahl
Fix
e
d free energ
y
with LJ-PME
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraham
Co
n
vert ins
t
all
g
uide to markdown
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraham
Merg
e
"Merge release-4-6 i
n
to release-5-0" into release
-
5-0
commit
|
commitdiff
|
tree
2014-06-29
Ber
k
Hess
Updat
e
d LJ-PME d
o
c
umentation
commit
|
commitdiff
|
tree
2014-06-29
Rossen Aposto
l
o
v
Use cosistent style w
h
en r
e
fe
r
ring to force fields
.
commit
|
commitdiff
|
tree
2014-06-29
T
e
e
m
u Murtola
Remo
v
e
s
o
m
e hardcod
e
d selection string b
u
ffers
commit
|
commitdiff
|
tree
2014-06-29
Roland Schulz
Fix detection of i386 in tm
p
i
commit
|
commitdiff
|
tree
2014-06-29
Erik
L
ind
a
hl
Enable rtp angle/di
h
edral en
t
ries no
t
connecte
d
by
.
.
.
commit
|
commitdiff
|
tree
2014-06-29
Mich
a
el Sh
i
rts
Allow prin
t
ing pote
n
tial energie
s
to dhdl
.
xvg file
commit
|
commitdiff
|
tree
2014-06-29
David va
n
der Spoel
Fixes
#
1
5
32, SEGV in
g_current
.
commit
|
commitdiff
|
tree
2014-06-29
Roland Schulz
Merge "Merge
b
ranc
h
'r
e
leas
e
-4
-
6' int
o
re
l
ease-5-0
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Roland Schulz
Fix error for no 64bit file suppo
r
t
commit
|
commitdiff
|
tree
2014-06-28
E
rik
Linda
h
l
Fixed CM
A
P generation f
o
r alanine dipeptide special
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Magnus Lundborg
Update T
N
G
build s
y
stem
commit
|
commitdiff
|
tree
2014-06-28
M
ark Abraham
Use p
a
rallel termin
o
logy mo
r
e cons
i
s
t
en
t
ly
commit
|
commitdiff
|
tree
2014-06-28
n
g
oga
Default SD inte
g
rat
o
r is now sd1 by Nicu
Goga
commit
|
commitdiff
|
tree
2014-06-27
Erik
L
in
d
ahl
Always s
e
t b-st
a
t
e
p
osres, even if
ide
n
tical
t
o a-state
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Updat
e
g_density to
h
a
ndle
b
ilayers better
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
F
ix L
J
PME Lorent
z
-Berthelot combin
a
tion rules
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apostol
o
v
Chan
g
ed linkin
g
order to make Extrae work
.
commit
|
commitdiff
|
tree
2014-06-27
Erik L
i
ndahl
Improve
P
DB I
/
O (
k
eep occup
a
ncy,
b
-factor, element)
commit
|
commitdiff
|
tree
2014-06-27
C
a
rst
e
n K
u
tzn
e
r
R
e
move obsolete p
u
ll-geometry opt
i
on 'posi
t
io
n
' from
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
Roland Schulz
F
i
x Phi Plat
f
o
rm f
i
l
e
for MP
I
commit
|
commitdiff
|
tree
2014-06-27
Erik
Lind
a
hl
Avoid warnings about coupling
when free_energ
y
=n
o
commit
|
commitdiff
|
tree
2014-06-27
Ros
s
en A
p
ostolov
A
d
ded
i
nfor
m
ation about di
h
edral res
t
ra
i
nts
.
commit
|
commitdiff
|
tree
2014-06-27
R
ossen Apostolo
v
Remove in
s
tall_manifest
.
txt
during make
clea
n
.
commit
|
commitdiff
|
tree
2014-06-26
M
a
r
k Abraham
M
erge "Merg
e
release
-
4-6 into release-5
-
0" into rel
e
as
e
-5-0
commit
|
commitdiff
|
tree
2014-06-25
Erik Lindahl
Updated A
m
ber GBSA parameters
commit
|
commitdiff
|
tree
2014-06-25
E
r
ik Lindahl
Make source c
o
m
pile
under Linux X32 ABI
commit
|
commitdiff
|
tree
2014-06-25
Erik Lindahl
Make it
h
arder fo
r
co
m
piler to optimize away SIMD
C
Make
.
.
.
commit
|
commitdiff
|
tree
2014-06-24
Mark Ab
r
a
h
a
m
Manual fixes
commit
|
commitdiff
|
tree
2014-06-24
Magn
u
s Lundbor
g
Improved check to decide i
f
to add chain/residue
.
commit
|
commitdiff
|
tree
2014-06-24
D
a
vid van der Spoel
Added check in grompp for shells and
inputrec issues
.
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Fix
e
d GROMOS assignment of P
R
O-NH terminu
s
torsions
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
M
a
ke
sure duplicates bondeds are set from hackblock
s
commit
|
commitdiff
|
tree
2014-06-24
Erik Lind
a
hl
Clean
u
p CMAP placement in p
a
rameter list
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Added mu
l
ti
s
imulation in
f
o to
l
og/
o
u
t
p
ut
commit
|
commitdiff
|
tree
2014-06-24
Rossen Ap
o
stolo
v
Exte
n
d
ver
s
ion c
h
eck
i
ng/warnings for checkpoint
con
t
inuation
commit
|
commitdiff
|
tree
2014-06-23
Rossen Apos
t
olov
Added tip5p to the l
i
st o
f
watermode
l
s in some FF
.
commit
|
commitdiff
|
tree
2014-06-23
E
rik Lindahl
Enable 4-letter res
n
ame in PDB ou
t
put, keeps more pdbin
f
o
.
commit
|
commitdiff
|
tree
2014-06-23
Erik
L
ind
a
h
l
Detect
non-fatal
warnings when trying C
F
lags for sourc
e
commit
|
commitdiff
|
tree
2014-06-23
E
r
i
k
Lindahl
Enable xvgr output and l
a
bels
f
or
g
_principal
commit
|
commitdiff
|
tree
2014-06-23
Erik Lind
a
hl
D
is
a
l
l
ow
extracting V
/
F
f
rom X
T
C
files in g_traj
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
War
n
if
using ns
t
eps=0 without co
n
tinua
t
io
n
=yes
commit
|
commitdiff
|
tree
2014-06-21
Vedran Miletić
Use
$
{CMAKE
_
INSTALL_LI
B
DIR} as
lib directo
r
y
for tng_io
.
.
.
commit
|
commitdiff
|
tree
2014-06-20
Berk Hess
Fix
g
_
mindist with pb
c
=XY
commit
|
commitdiff
|
tree
2014-06-20
Rossen Apo
s
tolov
Fixed ty
p
o in oplsaa ASPH charges
.
commit
|
commitdiff
|
tree
2014-06-20
Ro
s
sen A
p
ost
o
lov
Remov
e
d unused parame
t
ers
a
n
d cleanup o
f
inpu
t
rec
.
commit
|
commitdiff
|
tree
2014-06-19
Roland Sc
h
ulz
F
i
x
r
e
f error in cons
t
raint pull code
commit
|
commitdiff
|
tree
2014-06-19
Rossen Apos
t
olov
Small typos in surface tension d
e
scr
i
ption
.
commit
|
commitdiff
|
tree
2014-06-19
Magnus Lundborg
Bumped the TNG
li
b
r
ary to the
latest
v
ersio
n
.
commit
|
commitdiff
|
tree
2014-06-18
Erik Lindahl
Fixed CMake
2
.
8
.
12+ CUDA dyli
b
bug
s
an
d
wa
r
nings
on
.
.
.
commit
|
commitdiff
|
tree
2014-06-18
R
o
s
sen Ap
o
st
o
lov
Added reference to cm
a
p in pdb2gmx
.
commit
|
commitdiff
|
tree
2014-06-18
Berk Hess
Fixed sign
err
o
r in posres
d
vdl
commit
|
commitdiff
|
tree
2014-06-18
Mark Abraha
m
Made mdrun warn
w
hen generic kernels are used
commit
|
commitdiff
|
tree
2014-06-17
Carlo Camillon
i
F
ix a
R
eplica Exchange outp
u
t pro
b
lem
commit
|
commitdiff
|
tree
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