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Fixed pointer typo in patch from Alexey Shvetsov
2010-08-26
E
r
ik L
i
nd
a
hl
Fixed po
i
nter t
y
p
o
i
n p
a
tch from Alexey
S
hvet
s
ov
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindah
l
Added PBC
che
c
king patch t
o
g
_
clu
s
ter
from Alexey Shve
t
sov
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Li
n
dahl
Merge branch 'release-4-5-patches' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik
Lindahl
Mod
i
fied pdb2gmx
to
n
ot accept
e
xtra hydrogen a
t
o
m
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik L
i
ndahl
Merge branch 'release-4-5-patch
e
s
'
o
f git
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
tru
e
/false in
p
ut
s
ettings
should b
e
called bool instead
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
rik Lindahl
Merge
b
ranch 'rel
e
ase-4-5
-
patches' of git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Revert "Made pdb2gmx be sl
i
ght
l
y more
h
elpful when
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik Lindahl
U
p
d
ated completion
s
for 4
.
5 release
commit
|
commitdiff
|
tree
2010-08-26
Erik
L
indahl
Made /us
r
/local/gromacs default ins
t
allati
o
n path in
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Updated html documentatio
n
for
re
l
ease
4
.
5
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
Lind
a
hl
U
p
dated
m
a
n
ual pages, now with c
o
rre
c
t version (4
.
5
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k L
i
n
dahl
F
ix for warning
i
n ngm
x
makefile
commit
|
commitdiff
|
tree
2010-08-26
Erik Lind
a
hl
Changed versio
n
to beta4
commit
|
commitdiff
|
tree
2010-08-26
Erik L
i
ndahl
Updated scripts to produce 4
.
5 man
pages
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k Lindahl
Updated manpages for 4
.
5
releas
e
commit
|
commitdiff
|
tree
2010-08-26
Erik Linda
h
l
Remov
e
d useless g_logo and g_highwa
y
p
rograms
from
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik L
i
ndahl
g_
k
inetics removed
f
rom a
u
t
o
ma
t
ically b
u
ilt
program
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Fixed i
n
c
lu
d
e
p
ath in
vm
d
io
.
h
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Forgot to actually do t
h
e char->int change
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
r
ik Lindahl
Change
d
bool to
s
igne
d
i
n
teger
i
nstea
d
of unsigned
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Added m
i
ssing header include
commit
|
commitdiff
|
tree
2010-08-25
E
rik Lindahl
M
e
r
g
e bran
c
h 're
l
ease-4-5-
p
atc
h
es' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Eri
k
Lindahl
Made sure all source
files have some c
o
py
r
i
g
ht header
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik Li
n
dahl
Re-ad
d
ed op
e
nmm paper
commit
|
commitdiff
|
tree
2010-08-24
Erik Lindahl
Merge b
r
anch 'release-
4
-5-p
a
tche
s
' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Er
i
k
Lindahl
U
p
dated intel syn
t
ax x
8
6-64 as
m
fil
e
s to also support
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
ndahl
Fixe
d
uninitialized va
r
ia
b
l
e
error in GB k
e
rnel w
i
t
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik L
i
nda
h
l
Fixed
an unsigned/signed integer c
o
mparison
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed two more i
n
stances of strcasecmp->gmx_strc
a
secm
p
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k Lin
d
ahl
Copied
SSE intrinsics kernels from x86-64 to ia32
commit
|
commitdiff
|
tree
2010-08-22
Erik Li
n
d
a
hl
Replaced al
l
occurences of str(n)casecm
p
with gmx_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed
s
t
upid mistake where a statement was placed before
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
hl
R
e
pla
c
e
d test
i
ng of
git v
e
rsion with tes
t
ing for featur
e
s
commit
|
commitdiff
|
tree
2010-08-22
Erik
L
indahl
Fixed naming
problems
f
o
r double precision Fo
r
t
r
a
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed a typ
o
i
n
futil
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
M
e
r
g
e bra
n
ch 'release
-
4-5-patche
s
' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Cleaned up
a
ll ins
t
a
l
l
ed
h
e
aders to
remove
st
r
i
ct dependence
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lin
d
ahl
Removed
some unne
c
essar
y
#ifdefs
f
rom string
2
.
h; all
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k Lindahl
Amber
force fields now pass vali
d
ation
.
Beta stat
u
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
L
indahl
A
dd
e
d F77
k
ernel setup headers
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed
synchr
o
niza
t
i
o
n count
e
r
u
pdat
e
for f77 kernels
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed a bug for GB OBC born radius ca
l
c
u
l
ation in S
S
E2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixe
d
an uninitialized
v
ariable bug
commit
|
commitdiff
|
tree
2010-08-21
Erik Lind
a
hl
Fixe
d
a minor b
u
g
that caus
e
d Fort
r
an builds to
fail
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
rik
L
i
ndahl
Dont
w
r
i
te n
o
npolar surf
a
ce en
e
r
g
y
to energy
f
ile if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Lind
a
hl
Fixed
so Fortr
a
n kernels work
a
g
a
in
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Upgr
a
ded
to lat
e
st au
t
oco
n
f platform detec
t
ion
s
c
ripts
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
F
i
xed a chain rule error
i
n double
p
re
c
.
SSE2 GB for
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lind
a
hl
M
e
rge b
r
an
c
h 'release-4-5-patches' of g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
rik Lin
d
ahl
D
ouble preci
s
ion
S
S
E2
k
ernels for Generalized Born
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Updated GB SSE2 kerne
l
s, te
s
ting
in pro
g
ress n
o
w
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik L
i
ndahl
Merge b
r
a
n
ch '
r
e
lease-4-
5
-patche
s
'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Modi
f
ied atom order in Amber nucleotide
i
m
proper torsions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
i
k Lin
d
a
h
l
Modified improper torsion atom
order in
A
mbe
r
TRP residues
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Merge branch 're
l
ease-
4
-5-patches' of
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
ik Linda
h
l
Fix to
w
rit
e
GB and
s
u
rface energy to separate
t
erms
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
ik Lindahl
Merge branch '
r
elease-4-5-pa
t
c
h
es' of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik Lindahl
E
n
abled d
o
uble precision a
l
l-vs-all kernels
.
T
ested
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik Lindahl
Fixed simple typ
o
in
last commit
commit
|
commitdiff
|
tree
2010-08-18
Eri
k
Lindah
l
Fixed
p
revious
nasm-segv bug for
i
nt
e
l-syntax SSE in
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
L
ind
a
h
l
Fixed 64-b
i
t bu
g
in SSE
a
sse
m
bly (only visible with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
E
rik Li
n
d
ahl
W
orked a
r
ound an i
n
terna
l
c
ompil
e
r erro
r
for MS
V
C
when
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
L
indah
l
Merge branch 'release-4-5-patches'
o
f git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Deprecat
e
d -ins opti
o
n to g_hbond since
nobody se
e
ms
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lind
a
hl
Copied all
-
v
s
-all cha
n
g
e from x86
-
64 t
o
ia32
k
ernels too
commit
|
commitdiff
|
tree
2010-08-17
E
rik
Lindahl
Merge
b
ra
n
ch
'rel
e
ase
-
4
-
5-patches' of gi
t
.
grom
a
c
s
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Er
i
k Lin
d
a
h
l
Fixed
p
o
t
en
t
ial e
r
ror in
c
o
u
lomb ene
r
gy, an
d
maybe
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Li
n
d
ahl
Merge
branch 'release-4-5-pat
c
hes
'
of git
.
g
rom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lin
d
a
h
l
A
d
ded double prec
i
sion SSE2 gen
e
ralized born ker
n
e
ls
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Added ia32 al
l
-
v
s-all kern
e
ls
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
L
indah
l
Updated autocon
f
to wo
r
k with r
e
named SSE2 x86-64 asm
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
i
k Lindahl
Rena
m
e
d
S
S
E2 x86-64
asm test file to be consi
s
te
n
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
hl
Fix
e
d
typo to
de
t
ect b
o
t
h
x
8
6_64->i386
a
n
d
i
3
86->x8
6
_
6
4
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Merge
branch 'release-4-
5
-pa
t
ches' of
g
it
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
L
in
d
ahl
F
i
xed a namin
g
er
r
or introdu
c
e
d
ye
s
t
e
rday
in 32b
i
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik
Lindahl
Fi
x
ed compiler
e
rr
o
rs
for MSVC inlin
e
intrinsics and
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik L
i
ndahl
Fi
x
e
d chec
k
point problem in 32
b
its
.
We
shou
l
d
a
l
ways
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
L
i
n
dahl
Removed extra TER records after chains
w
e thin
k
are
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
hl
Merge branch
'
re
l
ease
-
4-5-patches' of
g
i
t
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lindah
l
F
i
xed
SSE kernels in double precision
f
or Cmake,
w
o
rking
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik L
i
ndahl
Merge branch 'release
-
4-5-patches' o
f
git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Lindahl
Cmake and Na
s
m suppo
r
t fo
r
windows
commit
|
commitdiff
|
tree
2010-08-10
E
r
ik Lindahl
Moved four more SS
E
assemb
l
y files t
o
avoid double
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Merge branch 'relea
s
e-4-5-patches' of
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Eri
k
Lind
a
hl
Chan
g
es to make Cmake work und
e
r win
d
ows
a
gain
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Ren
a
med i
n
tel synta
x
assem
b
ly files to
a
void
do
u
ble
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Added
N
A
S
M Cmake su
p
port
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
M
erge branch 'release-4-5-patches' of gi
t
.
g
r
omacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Eri
k
Lindahl
MAY
B
E a fix for Berk'
s
Heme pro
b
l
e
m
.
Ne
e
ds testin
g
commit
|
commitdiff
|
tree
2010-08-08
Erik Li
n
da
h
l
Merge b
r
a
n
c
h
'r
e
lease-4-5-p
a
t
c
he
s
' of git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-08
Erik Li
n
dahl
Added N
H
E as an Amber aminoaci
d
r
e
sidue type
commit
|
commitdiff
|
tree
2010-08-08
Erik Li
n
d
a
hl
Copie
d
CK-C
B
-N*-CT
A
mb
e
r i
m
proper to also list
C
K-CB
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lindahl
Merge branch '
r
elease-4-5-patches' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lindah
l
F
i
x
ed incorrec
t
#endif
-
> #
e
ls
e
that caused th
e
C all
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Merge bra
n
ch
'r
e
lease-4-5-
p
atches' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
E
r
i
k
L
i
n
d
a
hl
Fixed a
bug in ind
e
x generatio
n
for non-adjacent protein
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
E
r
ik Lindahl
Fixed nonexi
s
tent return type on gmx_
m
m_sincos_pd
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Added
o
ut int-extr
a
ction
m
acro to do
u
ble p
r
ecision
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Er
i
k Lindahl
Adde
d
double precis
i
o
n
SSE2 tr
a
nscendental functio
n
s
.
.
.
commit
|
commitdiff
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