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Moved buggy and unsupported g_sdf to contrib directory and removed its documentation...
2010-08-31
Erik Lindahl
Moved
b
uggy and unsu
p
ported g_sdf to contrib directory
.
.
.
commit
|
commitdiff
|
tree
2010-08-30
Erik Lin
d
ahl
Improved handli
n
g of
incl
u
d
e paths in gmxc
p
p from Teemu
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Adde
d
lo
n
ger list of aut
h
ors
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
rik Lindahl
Merge branch 'release-
4
-5-pa
t
ches' of git
.
gro
m
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lind
a
hl
Added c
h
eck for S
S
E2 s
u
p
p
ort to
u
s
e generali
z
e
d born
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik Lindahl
Added
trjconv check for
top
o
logy
prescence,
s
ee
b
ugz
i
lla
526
commit
|
commitdiff
|
tree
2010-08-27
Erik Linda
h
l
Merge branch 'release-4-5-patch
e
s'
o
f
git
.
gr
o
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
L
indahl
Fixed gmxcpp
to always use unix path sepa
r
ators
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Li
n
dahl
M
erge b
r
anch 're
l
ease-4-
5
-patches'
of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k
Lindahl
Fi
x
e
d
an
o
ther uninitialized v
a
riab
l
e warning in
gmx_ene
r
gy
.
c
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Add c
u
rrent path (
.
/) to topol
.
top i
n
clude
when
forc
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik L
i
n
dahl
Do
n
t write
E
OF warning
s
t
o st
d
out every time we c
h
eckpoint
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Li
n
dahl
Merge
b
ran
c
h '
r
ele
a
s
e
-
4-5
-
patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Fi
x
ed first
statemement occuring before variab
l
e dec
l
aration
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
Lindahl
M
erge br
a
nch 'release-4-5-
p
atches' of git
.
gr
o
m
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
i
k Linda
h
l
Modified pdb2gmx to automat
i
ca
l
ly
pick the force field
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik
L
i
n
dahl
Fixed pointer typo in patch from Alexey
S
hvetsov
commit
|
commitdiff
|
tree
2010-08-26
Erik
L
indahl
Added P
B
C checking patch t
o
g_clust
e
r from Ale
x
ey Shve
t
s
ov
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Merge branch 'release
-
4-5-patches' of
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
rik Lindahl
Modified pdb2gmx to not accept extra
h
ydro
g
en atom
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Mer
g
e br
a
nch 'r
e
l
e
a
s
e-4-5-patches' of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
true/
f
a
l
se input settings should be called b
o
ol
i
nstead
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Merge
b
ra
n
c
h
'release-4-
5
-patche
s
'
of git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
R
e
vert "Made pdb2gmx b
e
sl
i
ghtly more helpfu
l
when
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Updated completions for 4
.
5 rele
a
se
commit
|
commitdiff
|
tree
2010-08-26
Erik Li
n
dahl
M
a
de
/us
r
/lo
c
al
/
g
romacs
defa
u
lt
installation path in
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindah
l
U
pdated html document
a
tion for release 4
.
5
commit
|
commitdiff
|
tree
2010-08-26
Erik
Lind
a
hl
Update
d
manu
a
l
p
a
ges,
now with correct
version (4
.
5
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Fi
x
fo
r
warn
i
ng
in ngmx makefi
l
e
commit
|
commitdiff
|
tree
2010-08-26
E
rik L
i
ndahl
Changed vers
i
o
n
to beta4
commit
|
commitdiff
|
tree
2010-08-26
Erik Lind
a
hl
Upd
a
ted scr
i
pts
t
o pro
d
uce 4
.
5 man pages
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k Lindahl
Up
d
at
e
d
man
p
age
s
for 4
.
5
release
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
R
emove
d
useless
g_logo and
g_h
i
g
hway prog
r
ams from
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
g_kinetics r
e
moved
f
rom
a
utomatically
built p
r
og
r
am
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Linda
h
l
F
ixed include path in vm
d
io
.
h
commit
|
commitdiff
|
tree
2010-08-25
Erik
L
i
n
dahl
Forgo
t
to actuall
y
d
o
t
he char->int change
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Er
i
k Lindahl
Changed
b
ool to sig
n
ed integer instead of unsigned
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik
L
inda
h
l
Added m
i
s
s
i
n
g he
a
d
e
r
include
commit
|
commitdiff
|
tree
2010-08-25
E
r
i
k
L
inda
h
l
Merge branch
'release
-
4
-5-patches' of
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Er
i
k Lindahl
M
a
de sure
all source
f
iles have some
copyri
g
ht h
e
ader
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Eri
k
Li
n
da
h
l
Re-added openmm paper
commit
|
commitdiff
|
tree
2010-08-24
Erik Lindahl
M
e
rge branch 'relea
s
e-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik
Lindahl
Updated intel syntax x86-64 asm
f
iles
t
o
a
ls
o
suppor
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
Lind
a
hl
F
ixe
d
uninitialized
variable erro
r
in GB ke
r
nel wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik Lind
a
hl
Fixed an unsigned/
s
igne
d
in
t
e
ger co
m
parison
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
ndahl
F
ixed t
w
o more
i
nstances
o
f
s
trcasecmp->gmx
_
s
trcasecmp
commit
|
commitdiff
|
tree
2010-08-22
Erik Li
n
dahl
Cop
i
ed SSE intrinsics kernels
fro
m
x
8
6-64
t
o
i
a32
commit
|
commitdiff
|
tree
2010-08-22
Erik Li
n
da
h
l
R
e
placed all o
c
curences of str(n)casecmp w
i
th
g
mx_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed stupid mista
k
e
where a st
a
tement
was placed
b
e
f
ore
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Replaced testing of git ver
s
i
on with testing for features
commit
|
commitdiff
|
tree
2010-08-22
Erik Linda
h
l
F
i
xed nami
n
g problems fo
r
double pre
c
ision F
o
r
t
ran
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik Lindahl
Fi
x
ed a typo in futil
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
n
dahl
Merge branch 'release-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Clean
e
d
u
p al
l
installed
headers
to rem
o
ve strict dep
e
n
dence
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lindahl
Rem
o
v
e
d some unnecessary #ifdefs from string2
.
h; all
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindah
l
A
mbe
r
force fields now
pass vali
d
a
t
ion
.
Be
t
a statu
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
rik Lind
a
hl
Added F77
k
e
rnel
setup
h
eaders
commit
|
commitdiff
|
tree
2010-08-21
Erik L
i
n
dahl
Fixed synchroniz
a
t
i
on counter update for
f7
7
ke
r
nel
s
commit
|
commitdiff
|
tree
2010-08-21
Erik
Lindahl
Fixed a bu
g
for GB OBC born radius calculation in S
S
E
2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed a
n
uninitiali
z
e
d
variabl
e
bu
g
commit
|
commitdiff
|
tree
2010-08-21
Erik L
i
nd
a
hl
F
ixed
a
m
inor
bug that cau
s
ed Fo
r
tr
a
n b
u
ilds to
f
ail
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Dont
write nonpolar
s
urface energy to
e
nerg
y
file if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
rik Lin
d
ahl
Fixed so Fo
r
tran kern
e
ls work again
commit
|
commitdiff
|
tree
2010-08-21
E
r
ik Lindahl
Upg
r
aded to l
a
test autoconf
p
lat
f
orm
detection scripts
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed a chain r
u
l
e
error i
n
doubl
e
prec
.
SSE2
G
B for
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik L
i
ndahl
Merge br
a
n
c
h '
r
elease-4
-
5-patches' of
g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Li
n
dahl
D
oubl
e
p
rec
i
sion SSE2 ker
n
els for G
e
nera
l
ized Bo
r
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Li
n
da
h
l
U
p
date
d
GB SSE2 kernels, tes
t
in
g
in p
r
ogress now
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindah
l
Me
r
ge bran
c
h
'releas
e
-4-5-pa
t
ches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Modified ato
m
o
rder i
n
A
m
ber
nucleotide improp
e
r tor
s
ions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Eri
k
Lindahl
Modi
f
i
ed improper t
o
rsio
n
atom order in Amber TR
P
residu
e
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
Lindahl
Merge branch 'release-4-5-patches' of
git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Fix to write GB and s
u
r
face energy to separate term
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindah
l
M
e
rge branch
'
release-
4
-5-patches
'
of gi
t
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Eri
k
Lindahl
E
n
abled double precision al
l
-vs-all kernels
.
T
ested
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Fixed simp
l
e typo in last commit
commit
|
commitdiff
|
tree
2010-08-18
Erik
Lin
d
ahl
Fi
x
ed previo
u
s n
a
sm-segv b
u
g
for i
n
tel-syntax SSE
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
E
r
ik L
i
ndah
l
Fixed 64-
b
it bu
g
in SSE as
s
embly
(only v
i
s
ible with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Work
e
d around an inte
r
nal co
m
p
iler err
o
r fo
r
MS
V
C
w
h
en
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
Lin
d
ahl
Me
r
g
e
bran
c
h 'release-4-5-patches' of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Deprecated -ins optio
n
to g_hbond
sinc
e
nobo
d
y
seems
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Linda
h
l
Copie
d
a
ll-vs-all chan
g
e from x86-64 to ia32 ke
r
n
e
ls too
commit
|
commitdiff
|
tree
2010-08-17
E
rik
Lindahl
Merge branch
'
relea
s
e-4-5-patches' of
git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Er
i
k Lindahl
Fix
e
d potential error in
c
oulomb energy,
and ma
y
be
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
Merge branch
'
relea
s
e-4-5-pat
c
he
s
' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
A
d
de
d
doubl
e
preci
s
ion
SSE2 gen
e
r
alize
d
born kernel
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
Lindahl
A
d
ded ia32 all-v
s
-all ker
n
e
ls
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindahl
Updated autoconf to work w
i
th
r
enamed SSE2 x86-64 asm
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Li
n
dahl
Renamed
S
SE2 x8
6
-
6
4 asm test fi
l
e to be consistent
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
F
i
xed typo to
det
e
ct both x86_64
-
>i386 and i
3
8
6
->x
8
6
_
6
4
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Merge branch
'
re
l
e
a
se-4-5-patches' of
g
it
.
gro
m
acs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixed a naming erro
r
i
n
troduced ye
s
terday
in 32bit
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik L
i
ndahl
Fixed co
m
piler errors for MSVC in
l
ine int
r
insics and
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixed ch
e
ckpo
i
nt pro
b
lem in 3
2
bits
.
We
sho
u
ld alway
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
Lin
d
ah
l
R
e
moved extra TER records after chains we think are
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Er
i
k Lindahl
M
e
r
ge
b
ra
n
ch 'rel
e
ase-4-5
-
patc
h
es' of git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lin
d
a
hl
Fixed S
S
E kernels in double pre
c
is
i
on for Cmake, w
o
r
king
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik L
i
n
dahl
Merge
b
ranc
h
'rele
a
se-4-
5
-patches'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Lindahl
Cmak
e
and Nasm s
u
pport
for windows
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindah
l
Moved
four more SSE
assembly files
t
o
a
vo
i
d
double
.
.
.
commit
|
commitdiff
|
tree
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