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Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
2010-08-06
Erik
L
indahl
Merge branch 'release-4-5-
p
at
c
h
e
s' of git
.
groma
c
s
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lindahl
Fi
x
ed incor
r
ect #endif
-
>
#el
s
e t
h
at caused the C al
l
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik
Lindahl
Merge branch 'relea
s
e-4-5-patches' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Fixed a bug
i
n index g
e
neration f
o
r n
o
n-
a
dja
c
ent protein
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Fixed
n
on
e
xistent return type on
g
m
x
_mm_s
i
nc
o
s_pd
commit
|
commitdiff
|
tree
2010-08-04
Erik
L
i
nd
a
hl
Added out in
t
-ext
r
action macro to
double
p
recisio
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Eri
k
Lind
a
h
l
Added dou
b
le pr
e
cision SSE2 transcen
d
en
t
al functi
o
ns
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Er
i
k
L
indahl
Fixed
accura
c
y issues in gmx_mm_log
_
ps
(
)
, and added
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Erik L
i
nda
h
l
Modif
i
e
d
index process
i
n
g
to reinst
a
te
re
s
idu
e
-splitti
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Erik
L
indahl
Ad
d
e
d
i
o
n cla
s
ses to residu
e
types
.
dat
commit
|
commitdiff
|
tree
2010-07-30
Erik
L
i
nda
h
l
M
e
rge
b
ra
n
ch 'm
a
ster' of git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-30
E
rik Lindahl
Replac
e
d non-thread-safe
cal
l
s to ctime() with
our
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
E
rik Lindahl
Adde
d
portable gmx_ctime
_
r()
to enable repla
c
ement
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Lin
d
a
hl
M
e
rge bra
n
ch
'
maste
r
' o
f
git
.
gromacs
.
org:
g
r
om
a
cs
commit
|
commitdiff
|
tree
2010-07-30
Er
i
k
Li
n
dahl
Replaced localtime wit
h
localtim
e
_r() on
u
nix
and localtime_
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik
Lindahl
Merg
e
branch 'master' of
git
.
gromacs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-07-30
Erik
L
indah
l
Replace
d
r
e
add
i
r() with r
e
addi
r
_r(
)
t
o
a
v
oid future
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Me
r
g
e branch 'master' of g
i
t
.
groma
c
s
.
o
r
g
:
gromacs
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Po
r
ted x86-6
4
sing
l
e
precision S
S
E2 all-vs-all
p
atch
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lind
a
h
l
Commente
d
o
ut calls to do
u
ble pr
e
c
.
SSE2 a
l
l-vs-al
l
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Er
i
k L
i
nda
h
l
Worked around cross-inclusion problem betw
e
en grompp
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik L
i
ndah
l
R
e
m
oved d
e
precated nsb
.
h
header
commit
|
commitdiff
|
tree
2010-07-29
Erik L
i
ndahl
Merge
b
ranch 'mas
t
e
r' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-29
Erik Li
n
dahl
Ch
a
nged index group
analysis to only create water_and_ions
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
Merge br
a
n
c
h '
m
aste
r
'
of git
.
gromacs
.
o
r
g:gro
m
a
c
s
commit
|
commitdiff
|
tree
2010-07-29
Erik Li
n
dahl
Added res
i
duedefin
i
tions for water
,
and introd
u
ced
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik
L
inda
h
l
Reverted inco
r
r
ect Makefile
edit
e
arlier to
d
ay
commit
|
commitdiff
|
tree
2010-07-29
E
rik
L
indahl
Merge branch 'master' of
g
it
.
gromacs
.
org:gr
o
m
a
cs
commit
|
commitdiff
|
tree
2010-07-29
Eri
k
Lin
d
a
h
l
Imp
r
oved chain separation detection for p
d
b
2
gmx, and
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
Erik Lindahl
M
erge branch 'master' of g
i
t
.
gromacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-27
Erik Li
n
dahl
Added missing double prec
.
SS
E
2 header file
commit
|
commitdiff
|
tree
2010-07-27
E
rik
Lindahl
T
emporarily disable
d
a ne
w
pdb
2
gmx
opti
o
n
commit
|
commitdiff
|
tree
2010-07-27
Erik Lindahl
M
odi
f
i
ed PD
B
io cod
e
to mer
e
ly stor
e
the chain _identif
i
er
_
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
E
rik Lin
d
ah
l
A
d
ded lot
s
o
f missing cmake
d
efines to
config
.
h
.
c
m
a
kein
commit
|
commitdiff
|
tree
2010-07-26
Erik Linda
h
l
Ad
d
ed lots of header cmakedefin
e
s
to config
.
h
.
cm
a
kein
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Erik
L
ind
a
hl
Mer
g
e bran
c
h
'ma
s
te
r
' o
f
git
.
g
r
omacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-26
Erik Lindahl
Adde
d
N
ME
t
o th
e
list of amino acid n
a
mes
commit
|
commitdiff
|
tree
2010-07-26
Erik
L
i
n
d
ahl
pdb2gmx now
a
p
p
lies termini to the first/last residues
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Erik
Lindahl
Added g
b
sa
.
itp to Makefile
.
am in all
am
b
er force field
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Er
i
k Lindahl
Cha
n
ged t
o
n
o
n-prefixed
d
efau
l
t RNA
res
i
due
n
ames
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Er
i
k Lindahl
Merge branch '
m
aster'
o
f git
.
grom
a
cs
.
o
rg:
g
ro
m
acs
commit
|
commitdiff
|
tree
2010-07-26
Erik
L
indahl
Changed to non-prefixed defa
u
lt RNA residue n
a
mes
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Eri
k
Lindahl
M
e
rge
bra
n
ch 'master'
o
f
git
.
gromacs
.
org:g
r
om
a
cs
commit
|
commitdiff
|
tree
2010-07-26
Erik Lindahl
Adde
d
f
i
les in
prep
a
ration o
f
double-precision
AllvsAll
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Erik Li
n
dahl
Add
e
d
gbsa parameters to Amber force fi
e
lds
commit
|
commitdiff
|
tree
2010-07-25
Eri
k
Li
n
dahl
Resolved merge conflict
commit
|
commitdiff
|
tree
2010-07-25
Erik Linda
h
l
Fixed bug for smal
l
systems in al
l
-v
s
-all kernels,
.
.
.
commit
|
commitdiff
|
tree
2010-07-25
Erik Lindahl
Ad
d
ed DN
A
/RN
A
re
s
idue tra
n
slation
t
a
bles for cha
r
mm27
commit
|
commitdiff
|
tree
2010-07-25
Erik Lindah
l
Enforce r
u
le a
b
ou
t
matching rtp and tdb names to non
.
.
.
commit
|
commitdiff
|
tree
2010-07-25
Erik
Lindahl
Added autoconf and cmake checks to m
a
ke the restrict
.
.
.
commit
|
commitdiff
|
tree
2010-07-25
Erik Lind
a
hl
Added a PO
S
IX/Window
s
portab
l
e
way t
o
s
can dir
e
ctories
.
.
.
commit
|
commitdiff
|
tree
2010-07-24
Erik Lindahl
Second ba
t
ch of file modificat
i
ons to
e
nable A
m
ber
.
.
.
commit
|
commitdiff
|
tree
2010-07-24
Erik Lindahl
p
db2gmx
c
h
anges to support prot
e
i
n/DNA/RNA mixture
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Erik Lindahl
Remove pro
p
er
t
o
rsi
o
n
s
with
zero force co
n
stant at
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Erik Li
n
dahl
Removed scratch files f
r
om amb
e
r
99
commit
|
commitdiff
|
tree
2010-07-21
Erik Lindahl
F
ixed bug
s
that caused type-4 i
m
propers (same
f
orm
.
.
.
commit
|
commitdiff
|
tree
2010-07-21
Erik Lindahl
Changes to enable
Am
b
er99
commit
|
commitdiff
|
tree
2010-06-23
Erik Lin
d
ahl
Added g
c
c
4
1 chec
k
commit
|
commitdiff
|
tree
2009-12-16
Erik Lind
a
hl
Manual
a
pp
l
ication of patch 5c076c352b4c8a43
b
5
2ab441691
9
3
2
ef
.
.
.
commit
|
commitdiff
|
tree
2009-12-16
Erik L
i
ndahl
M
e
rge bran
c
h 'release-4-0-patches'
of gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2009-12-16
Er
i
k Lindahl
Rem
o
ved def
a
ult nice-19
behavior fro
m
mdr
u
n even
on
.
.
.
commit
|
commitdiff
|
tree
2009-12-12
Erik Lindahl
Replaced ac
o
s
-based meth
o
d
f
or calc
u
latin
g
angles
b
e
t
ween
.
.
.
commit
|
commitdiff
|
tree
2009-12-11
Erik Lindah
l
Fixed signed
/
unsign
e
d
comp
a
rison m
i
smatch
in
scanner
.
.
.
commit
|
commitdiff
|
tree
2009-12-11
Erik Lin
d
ahl
Merge branch 'm
a
ster' o
f
git
.
g
r
omacs
.
org:grom
a
c
s
commit
|
commitdiff
|
tree
2009-12-11
Erik Lind
a
h
l
Fixed errors
in vmdio
.
c whe
n
compiled wi
t
h
MSVC8
,
6
4
bi
t
commit
|
commitdiff
|
tree
2009-12-06
Erik Lindahl
Add
e
d ch
e
ck
for 3dnow
that was remo
v
e
d when merg
i
ng
.
.
.
commit
|
commitdiff
|
tree
2009-12-06
Erik Lindahl
Added auto-detectio
n
for 6
4
bit su
p
p
o
rt
o
n m
a
cs
commit
|
commitdiff
|
tree
2009-12-04
Er
i
k
L
indahl
typo i
n
name for gmx_m
m
_casts
i
128_ps()
commit
|
commitdiff
|
tree
2009-12-04
Er
i
k Lindahl
Fixed gromacs
w
rapper fo
t
_mm_
c
astsi128_ps intrins
i
c
.
.
.
commit
|
commitdiff
|
tree
2009-12-03
Erik Lind
a
hl
Committed all
-
a
n
gle-con
s
t
r
a
i
n
t
fix from Peter
Ea
s
tman
.
.
.
commit
|
commitdiff
|
tree
2009-12-03
E
r
ik
L
indahl
C
o
mmitted
a
ll-angle
-
constraint fix f
r
o
m Peter Eastman
.
.
.
commit
|
commitdiff
|
tree
2009-12-03
Erik Lindahl
Enabled separa
t
e P
M
E
nodes(threads) w
i
th t
h
re
a
d-mpi
.
.
.
commit
|
commitdiff
|
tree
2009-12-02
Erik Lind
a
hl
Mer
g
e
branch
'
maste
r
' of
g
it
.
g
r
omacs
.
or
g
:
g
romacs
commit
|
commitdiff
|
tree
2009-12-02
Erik Lind
a
h
l
F
i
xed mute
x
d
e
a
dlock in
gmx_fseek
commit
|
commitdiff
|
tree
2009-11-30
E
rik Lindahl
removed debug print-statement
commit
|
commitdiff
|
tree
2009-11-30
Erik Lindahl
Added FFT
c
ode fr
o
m Ro
l
a
n
d
commit
|
commitdiff
|
tree
2009-11-30
Erik Lindah
l
I
nita
l
2D PME decomposition changes
commit
|
commitdiff
|
tree
2009-10-21
Erik Lindahl
M
e
rge branch 'maste
r
'
o
f git
.
groma
c
s
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2009-10-21
Erik
L
in
d
ahl
R
e
mov
e
d charmm files from git for now, since it wont
.
.
.
commit
|
commitdiff
|
tree
2009-10-08
Erik Lindahl
Fixed MS
V
C
b
u
ild errors
commit
|
commitdiff
|
tree
2009-10-08
Erik Lin
d
ahl
Merge branch 'mas
t
er'
of
git
.
gromacs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2009-10-08
Erik
L
inda
h
l
U
p
dat
e
d SSE2 intrinsics in
p
reparation
for new kerne
l
s
.
commit
|
commitdiff
|
tree
2009-10-07
Erik Li
n
dahl
Fi
x
ed memo
r
y leak
s
in su
r
face
c
o
d
e
commit
|
commitdiff
|
tree
2009-10-05
Erik
L
ind
a
hl
Moved
s
t
a
tic v
a
riab
l
es
i
n pme
.
c
into gmx_pme_t structure
.
.
.
commit
|
commitdiff
|
tree
2009-09-27
Er
i
k
Lindahl
A
dded auto-d
e
tection for
6
4bit su
p
po
r
t on mac
s
commit
|
commitdiff
|
tree
2009-09-27
Erik
L
i
n
d
a
hl
E
nab
l
ed file t
r
uncation on windows
commit
|
commitdiff
|
tree
2009-09-27
E
r
ik Lindahl
F
i
xed
non-portab
l
e POSIX
r
outines to work under windows
commit
|
commitdiff
|
tree
2009-09-27
Er
i
k Lindahl
Fixed more head
e
rs for MSVC cmake
b
uild
s
commit
|
commitdiff
|
tree
2009-09-27
Erik Lind
a
hl
Fi
x
ed header
f
or cmake sse2 allvs
a
ll ker
n
els
commit
|
commitdiff
|
tree
2009-09-27
Erik
L
i
n
dahl
A
dded dummy variables to av
o
id warn
i
ngs about
emp
t
y
.
.
.
commit
|
commitdiff
|
tree
2009-09-27
E
rik Lindahl
Disabled prestepping in gmx_tune_pme,
since it r
e
lies
.
.
.
commit
|
commitdiff
|
tree
2009-09-27
E
rik
L
i
n
dahl
Added
files to re-enab
l
e
cma
k
e builds with all-vs-all
.
.
.
commit
|
commitdiff
|
tree
2009-09-25
Erik
Lindahl
Merge br
a
nch 'master' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-09-25
Erik
L
indahl
Fix
e
d invsqrt->gmx_invsqrt for a singl
e
routine
commit
|
commitdiff
|
tree
2009-09-09
E
r
ik
L
indahl
F
i
x f
o
r double precisi
o
n SSE2
code with ge
n
bor
n
(compile
.
.
.
commit
|
commitdiff
|
tree
2009-09-09
Erik L
i
ndahl
Me
r
ge
b
ranch
'
ma
s
ter' of git
.
gromacs
.
o
r
g:g
r
o
macs
commit
|
commitdiff
|
tree
2009-09-09
Erik Lindahl
N
e
w
al
l
-vs-all l
o
ops and worki
n
g SSE gb ke
r
ne
l
s
+radii
.
.
.
commit
|
commitdiff
|
tree
2009-08-31
E
rik Lindah
l
Merge branch 'm
a
ster' of
g
it@git
.
g
r
omacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-08-31
Erik Lindahl
Change
s
to
h
ave GB det
e
ct 1-2,1-3,1-4 params from exclusions
commit
|
commitdiff
|
tree
2009-08-30
Erik
Lindahl
Init
i
a
l all-vs-all kernels
.
Single precision SSE
w
orkin
g
.
commit
|
commitdiff
|
tree
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