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Updated GB SSE2 kernels, testing in progress now...
2010-08-18
E
r
ik
Lindahl
U
pdat
e
d GB SSE2 ke
r
nel
s
,
testing in progress no
w
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lin
d
a
hl
Merge br
a
nch
'release
-
4-5
-
pat
c
hes'
of git
.
gro
m
acs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
rik Lindahl
Modified atom order i
n
A
m
ber nucleo
t
ide improp
e
r
t
orsions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
ri
k
Lindahl
Modified impro
p
er t
o
rsion atom or
d
er i
n
A
mber T
R
P residues
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Linda
h
l
Merge branch
'release-4-
5
-patches' of git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
Lindahl
Fi
x
to writ
e
GB and sur
f
ace
e
n
e
r
g
y
t
o
separate terms
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
i
ndahl
Merge branch 'r
e
lease-4-5-
p
atches' of git
.
gro
m
acs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Enabl
e
d
do
u
ble precision all-vs-all
k
ernels
.
Tested
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
ri
k
Linda
h
l
Fixed simple typo
i
n
l
a
s
t
commit
commit
|
commitdiff
|
tree
2010-08-18
Erik Lin
d
ahl
Fi
x
e
d
pre
v
ious nas
m
-segv
b
u
g for
i
ntel-s
y
ntax S
S
E in
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Fix
e
d
6
4-bit bug
i
n SSE
asse
m
bly (o
n
ly v
i
sible with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
L
ind
a
hl
Wor
k
e
d
a
rou
n
d an internal compiler error fo
r
MSVC when
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
Lindahl
M
erge branch 'release-
4
-5-
p
a
t
ches' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Deprecated -ins option to g_hbond since
nobo
d
y seems
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Cop
i
ed all-vs-all
c
h
a
n
ge from x86-64 to ia32 kernels too
commit
|
commitdiff
|
tree
2010-08-17
Erik
Lindahl
Mer
g
e branch '
r
el
e
ase-4-5-patches' of git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Fixed pote
n
tial error in
c
oulomb ene
r
gy, and may
b
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
Lindahl
Merge
b
r
anch 'release
-
4
-
5-pa
t
che
s
'
of git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
Lindahl
Ad
d
ed double
precision
S
S
E
2 generali
z
e
d
born kernels
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Er
i
k
L
indahl
Added ia32 all-vs-all ke
r
ne
l
s
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
h
l
Updated autoconf to work wit
h
renamed SSE2 x86-
6
4 asm
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik L
i
ndahl
Renamed S
S
E
2 x86-64 asm test file
t
o be c
o
n
sistent
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixed typo to d
e
te
c
t bo
t
h x86_64->
i
386 an
d
i386-
>
x86_64
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lind
a
h
l
Merge br
a
nch 'releas
e
-4-
5
-p
a
t
c
hes' o
f
git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Li
n
dahl
Fixed a
n
aming err
o
r in
t
roduced yes
t
erday in 32bit
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Linda
h
l
Fixed
compiler errors for M
S
VC inline intrinsics
and
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
Li
n
d
a
hl
Fixed checkpoint proble
m
in
3
2 bits
.
We should
a
lways
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik Lindahl
Removed
extr
a
TE
R
r
eco
r
d
s
after chains we think are
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Eri
k
Lin
d
ahl
Merge branch
'release-
4
-5-
p
atches' of gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik Lindahl
Fixed
SS
E
ke
r
nel
s
i
n double p
r
eci
s
ion
f
or
C
m
ake, working
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Linda
h
l
Merge branch 'releas
e
-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik L
i
ndahl
Cmake and Nasm suppor
t
for
wi
n
do
w
s
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Moved
four m
o
re SSE as
s
e
m
bly files t
o
avoid double
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Merge branch 'release-4-
5
-patc
h
es'
of g
i
t
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Cha
n
ges to make Cmake wo
r
k under win
d
ows again
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Renamed intel s
y
n
t
ax a
s
sembly
files t
o
avoi
d
double
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Li
n
dahl
A
d
d
ed NASM Cma
k
e
suppo
r
t
commit
|
commitdiff
|
tree
2010-08-10
E
rik Lindahl
Mer
g
e branch
'
release-4-5-patches'
of git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
MAYBE a fix for Be
r
k's Heme problem
.
Ne
e
ds te
s
ting
commit
|
commitdiff
|
tree
2010-08-08
Erik Lindahl
Me
r
ge branch
'
rel
e
ase-4-5-pat
c
hes' of git
.
grom
a
cs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-08
E
r
ik Li
n
da
h
l
Added NHE as an Amber a
m
i
n
oa
c
id r
e
sidue ty
p
e
commit
|
commitdiff
|
tree
2010-08-08
Erik Lindahl
Cop
i
ed CK-C
B
-
N*-CT Amber improper t
o
also
l
ist CK-CB
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lindah
l
M
erge branch 'rel
e
ase-
4
-5-patch
e
s' of git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Lind
a
h
l
Fixed incorrect #endif -> #else that
c
aused
t
he C all
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Mer
g
e branc
h
'release-4-5-patches' of git
.
g
r
omacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Er
i
k Lin
d
ahl
Fixed
a
bu
g
in index generation for non-adj
a
cent pro
t
ei
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindah
l
Fixed n
o
ne
x
ist
e
nt return t
y
pe
on gmx_mm_s
i
ncos_pd
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
A
d
ded out i
n
t-e
x
traction macro to
double prec
i
sion
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Linda
h
l
Add
e
d double p
r
ecisi
o
n S
S
E2 transcendental f
u
nctions
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindah
l
Fixed accuracy issues in gmx_mm_log_ps(), and adde
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Erik
L
i
n
d
ahl
Merge branch 'rel
e
a
se-4-5-patche
s
' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Erik Lindahl
Modified TER record wr
i
ting behav
i
our
(
onl
y
add aft
e
r
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Er
i
k Lindahl
Merge branch 'release-4-5-
p
a
tches' of g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Er
i
k Lin
d
ahl
Fi
x
ed b
u
ild issu
e
for te
m
plate progr
a
m in double pr
e
cision
commit
|
commitdiff
|
tree
2010-08-02
Erik Li
n
dahl
Removed
u
nused variable tha
t
cau
s
ed
a warning
commit
|
commitdiff
|
tree
2010-08-02
Erik Lindah
l
Tem
p
or
a
rily disabled double p
r
ec
i
sion SSE2 generaliz
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
E
rik L
i
ndahl
F
i
xed error in (unus
e
d)
S
SE2 doub
l
e pr
e
cision inlin
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Erik
L
indahl
M
o
difie
d
in
d
ex processing to
r
e
instate re
s
idue-splitting
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Eri
k
Lindahl
Added ion classes to
r
esiduet
y
p
es
.
dat
commit
|
commitdiff
|
tree
2010-07-30
Erik Li
n
d
a
hl
M
erge branch 'master' of
git
.
gromacs
.
org:g
r
om
a
cs
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Replaced non-thre
a
d-safe call
s
to ctim
e
(
) with our
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik L
i
n
dahl
Adde
d
portable gmx_
c
time_r() to enab
l
e replacement
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Er
i
k Lindahl
Merge b
r
anch 'ma
s
t
er
'
of g
i
t
.
gr
o
macs
.
o
rg
:
g
r
oma
c
s
commit
|
commitdiff
|
tree
2010-07-30
Erik L
i
n
d
a
h
l
Replaced
loca
l
time with lo
c
al
t
ime_r() on unix and localtime_
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Er
i
k Lindahl
Mer
g
e br
a
nch 'master' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-30
Erik
L
inda
h
l
Replace
d
readdir() with re
a
ddir
_
r() to avoid
f
uture
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Merge bra
n
ch 'master
'
of git
.
gromac
s
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Ported x
8
6-64 single preci
s
ion S
S
E
2 all-v
s
-all patch
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
C
o
m
m
ented out calls to
d
ouble p
r
e
c
.
SSE2 all-vs-a
l
l
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
W
ork
e
d a
r
ound cross-inclusion problem be
t
ween grompp
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
R
e
moved deprecated nsb
.
h
hea
d
er
commit
|
commitdiff
|
tree
2010-07-29
Er
i
k Lindahl
Mer
g
e branch
'
master' of
gi
t
.
gromacs
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
Changed index group
an
a
ly
s
is to on
l
y
cr
e
ate water_and_ions
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
Me
r
ge branch 'mast
e
r' of git
.
grom
a
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
Added residu
e
defi
n
i
t
ions for
wate
r
, and
introduced
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
Reverted inc
o
rrect
M
a
kefile edit e
a
rli
e
r
today
commit
|
commitdiff
|
tree
2010-07-29
Erik
Lindahl
Me
r
g
e
branch '
m
aste
r
' of git
.
gromacs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-07-29
Er
i
k
L
indahl
Improved chain separation dete
c
tion for pdb
2
g
m
x, and
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
E
r
ik Lind
a
hl
Merge branch 'mas
t
er' of git
.
gromacs
.
o
rg:
g
r
omacs
commit
|
commitdiff
|
tree
2010-07-27
E
r
ik Linda
h
l
Added missing
d
ouble prec
.
SSE2 header
f
ile
commit
|
commitdiff
|
tree
2010-07-27
E
r
ik L
i
nd
a
hl
T
e
mp
o
rar
i
ly disabled a new p
d
b2gmx o
p
tion
commit
|
commitdiff
|
tree
2010-07-27
E
r
ik
L
in
d
a
hl
Modified PDB io cod
e
t
o
m
e
r
e
ly
s
tore
the chain _identifier_
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Erik L
i
ndahl
A
d
ded
l
ots
o
f mi
s
sing cmakedefi
n
es to config
.
h
.
cm
a
kei
n
commit
|
commitdiff
|
tree
2010-07-26
E
rik Lind
a
hl
Added lots of header cmak
e
defi
n
es
t
o config
.
h
.
cmakein
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Erik
Lindahl
Me
r
ge branch
'mast
e
r' of git
.
gr
o
macs
.
o
r
g:g
r
omacs
commit
|
commitdiff
|
tree
2010-07-26
Erik Li
n
dahl
Adde
d
NME to the list of amino acid name
s
commit
|
commitdiff
|
tree
2010-07-26
Er
i
k Lindahl
pdb
2
gmx now applies
t
e
rmini to the first/last
res
i
dues
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Eri
k
Linda
h
l
Added
gbsa
.
itp to Ma
k
efil
e
.
am in
all
amber f
o
rce fields
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Er
i
k Lin
d
ahl
Change
d
to n
o
n-
p
r
e
fixed default
RNA residue names in
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
E
r
ik Lindahl
Merge b
r
anch '
m
ast
e
r' of
g
it
.
g
r
omacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-07-26
Erik L
i
ndahl
Ch
a
nged
to non-prefixed de
f
ault RNA
r
esidue names in
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
E
r
ik Lindahl
Merge branch 'master' of git
.
g
roma
c
s
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-07-26
Erik
L
indahl
Added
files in
pr
e
pa
r
a
t
ion o
f
d
ouble-pre
c
ision Allv
s
A
l
l
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Erik Linda
h
l
Added gbs
a
parameters
t
o
Amber force fields
commit
|
commitdiff
|
tree
2010-07-25
Er
i
k
L
ind
a
hl
Resolve
d
merge conflict
commit
|
commitdiff
|
tree
2010-07-25
E
r
ik
Li
n
dahl
Fixe
d
bu
g
for
small syste
m
s in al
l
-
vs-all kernels,
.
.
.
commit
|
commitdiff
|
tree
2010-07-25
Erik L
i
ndahl
Adde
d
DNA/RNA r
e
sidue t
r
anslation tables for charmm27
commit
|
commitdiff
|
tree
2010-07-25
Erik Lindahl
Enforce rule about matc
h
ing rtp and tdb names to
n
on
.
.
.
commit
|
commitdiff
|
tree
2010-07-25
Erik
L
indahl
Added
autoconf and
cma
k
e checks to make the
restrict
.
.
.
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2010-07-25
Erik Li
n
dahl
Added a
P
OSIX/Wi
n
d
o
ws p
o
rta
b
le way to
s
can
director
i
es
.
.
.
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