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Fixed potential error in coulomb energy, and maybe segfaults for small molecules...
2010-08-17
Erik Lin
d
ah
l
Fixed potential erro
r
i
n
coulomb
e
nergy
,
a
n
d maybe
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik L
i
ndahl
Merge
b
ranch 're
l
e
ase-4-5-pat
c
hes'
o
f git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Lin
d
ahl
Ad
d
ed double precisi
o
n SSE2 genera
l
i
zed born kernels
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Added ia32 all-vs-al
l
k
e
rnels
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Updated autoconf to w
o
rk with rename
d
SSE2 x86-
6
4
a
sm
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik Lindahl
R
e
named SSE2 x86-
6
4 as
m
te
s
t file to be consistent
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
hl
Fixed typo
to detect both x86_
6
4-
>
i386 an
d
i38
6
->x86_64
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Linda
h
l
Merge bra
n
ch
'
release-4-5-pa
t
ches' of
g
it
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixed a naming
e
r
ror introduc
e
d yesterday i
n
32bit
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fi
x
ed compiler er
r
ors for MSVC i
n
line in
t
r
insics and
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik
L
i
n
d
ahl
Fixed checkpoint problem in 32 bits
.
We should always
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Er
i
k Linda
h
l
Removed e
x
tra TER records after
chain
s
we think are
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Li
n
dahl
M
e
rge branch 'release-4-5-pa
t
ches' of git
.
grom
a
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
F
ixed SSE kernels in double precisi
o
n for Cm
a
ke, wor
k
ing
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Erik Lindahl
Merg
e
branch 'release-4-5-patches
'
of
git
.
gro
m
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
E
r
i
k Lindahl
Cmake and
N
asm
suppo
r
t
for
windows
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Moved four more SS
E
as
s
e
mbly files to avoid double
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Merge br
a
nch 'release-4-5-patches' of git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Change
s
to make Cma
k
e work
u
nder windows again
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Re
n
amed i
n
tel syntax assembly files to avoid double
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Ad
d
e
d
NASM C
m
ake support
commit
|
commitdiff
|
tree
2010-08-10
Erik Lindahl
Merge branch '
r
e
l
ease-4-5-pat
c
hes'
of git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Eri
k
L
i
ndah
l
M
AYBE a
fix for Berk
'
s
Heme p
r
oblem
.
Needs
t
esting
commit
|
commitdiff
|
tree
2010-08-08
E
r
i
k
Lindah
l
Merge branch 'release-
4
-5-patche
s
' of git
.
gro
m
acs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-08
Erik Lindahl
A
d
ded NHE
as
a
n
A
m
b
er amin
o
acid residue type
commit
|
commitdiff
|
tree
2010-08-08
Eri
k
Lind
a
hl
C
o
pied
CK-CB-N*-C
T
Amber impr
o
p
e
r to also
list CK
-
C
B
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik
Lindahl
Mer
g
e branch 'release-4-
5
-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-06
Erik Linda
h
l
Fixed incorrect #e
n
dif -> #els
e
that ca
u
se
d
the C a
l
l
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Eri
k
Lindahl
M
e
rge bra
n
ch 'release-4-5-patches
'
of git
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
E
r
ik Lindahl
Fixed
a
bug in index
gene
r
ation
f
o
r
non-adjacent prot
e
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Fixed nonexistent return type on gmx_mm
_
sincos_pd
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
A
d
ded out in
t
-extrac
t
ion macro to double prec
i
sion
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
Erik Lindahl
Added double precision SSE2
transc
e
nde
n
t
a
l fu
n
ct
i
ons
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
E
r
ik Li
n
d
a
hl
Fixed accuracy
i
ssues i
n
g
m
x_mm_log_ps()
,
an
d
add
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Erik L
i
ndahl
Merge
bra
n
ch 'release-4-5-pa
t
ches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Erik Lin
d
ahl
Modifi
e
d TER reco
r
d writing behaviour (only add
after
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Erik
L
indahl
Mer
g
e branch 'release-4-5-patche
s
'
of gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
E
ri
k
Linda
h
l
Fixed bui
l
d issue
f
or template progr
a
m in double
p
r
e
cision
commit
|
commitdiff
|
tree
2010-08-02
Eri
k
L
indahl
Rem
o
ved unused variable that
c
aused a warning
commit
|
commitdiff
|
tree
2010-08-02
E
rik L
i
nda
h
l
Temporarily disabled d
o
uble pr
e
ci
s
io
n
S
SE2 genera
l
i
z
ed
.
.
.
commit
|
commitdiff
|
tree
2010-08-02
Er
i
k
L
indahl
Fixed e
r
ror in (unused) SSE2 do
u
bl
e
p
r
ecision
i
n
l
ine
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Erik Lind
a
hl
Modifie
d
i
n
d
e
x processi
n
g to reinstate residue-s
p
litting
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
Erik Lindahl
Added i
o
n
clas
s
es to res
i
d
u
e
t
ypes
.
dat
commit
|
commitdiff
|
tree
2010-07-30
Erik Lin
d
ahl
Merge
b
ranch 'master' of
git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-30
E
rik Lindahl
Re
p
la
c
e
d non-
t
hread-safe calls to ctime() with our
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Linda
h
l
Added p
o
r
t
abl
e
gmx_ctime_
r
()
to ena
b
le replac
e
ment
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Eri
k
Lindahl
M
e
rge branch 'master' of git
.
gr
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-30
E
ri
k
Lind
a
hl
R
e
placed localt
i
m
e
with localtime
_
r
() o
n
unix an
d
localtime_
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik Lin
d
ahl
Merge branch 'master
'
of git
.
gr
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-30
Erik Lindahl
Rep
l
a
c
ed read
d
ir() with readdir_r() to
a
v
oi
d
future
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Erik
L
indahl
Merge branch 'master' of git
.
gro
m
acs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-30
Erik L
i
n
d
ahl
P
orted
x
86-6
4
singl
e
precision SSE2 all-vs-all
p
atch
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
E
r
ik Lindahl
Commented
o
ut calls to d
o
u
b
le
p
r
ec
.
SSE2 a
l
l-v
s
-all
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
E
rik Lindahl
Worked around cro
s
s-inclusion p
r
oblem between
g
romp
p
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
Removed deprecated nsb
.
h header
commit
|
commitdiff
|
tree
2010-07-29
E
r
ik
Lind
a
hl
Merge branch 'master' o
f
git
.
gromacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
C
hanged index
g
r
o
up
ana
l
ysis
to only
c
r
eate water_
a
nd_ions
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
M
erge br
a
nch 'master'
o
f
git
.
groma
c
s
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-07-29
Er
i
k Lind
a
hl
Adde
d
r
esiduedefinitions
for wat
e
r, an
d
i
n
t
roduced
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Erik Lindahl
Re
v
e
r
ted incorrect Makefile edit
e
arlie
r
toda
y
commit
|
commitdiff
|
tree
2010-07-29
Erik Li
n
d
a
h
l
Merg
e
branch
'master' of git
.
gromacs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-07-29
Er
i
k Lindahl
Impr
o
ved chain separ
a
tion detect
i
on for p
d
b2gmx, and
.
.
.
commit
|
commitdiff
|
tree
2010-07-27
E
ri
k
Lindahl
Merge bran
c
h 'master'
o
f git
.
gro
m
a
cs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-07-27
Erik Lindahl
Added missing do
u
ble prec
.
SSE2 header
file
commit
|
commitdiff
|
tree
2010-07-27
Erik Lindahl
Temporar
i
ly di
s
abled a
n
e
w pdb2gmx
op
t
i
o
n
commit
|
commitdiff
|
tree
2010-07-27
Erik Lindahl
Mo
d
ifie
d
PDB io c
o
de t
o
merely store t
h
e chai
n
_ident
i
f
i
e
r_
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Erik Lindahl
Added lots of mi
s
sing
c
makedefine
s
t
o config
.
h
.
c
m
akein
commit
|
commitdiff
|
tree
2010-07-26
Erik Lindahl
Adde
d
l
ots o
f
header cmakedefi
n
es to
c
o
n
f
ig
.
h
.
cmakein
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Erik Lind
a
hl
M
erge branch
'
maste
r
'
o
f
git
.
gromacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-26
Eri
k
Lindahl
Added
NME to the list
of amino a
c
id names
commit
|
commitdiff
|
tree
2010-07-26
Erik Linda
h
l
pdb2gmx now applies
t
e
r
mini to the first/la
s
t
r
esidues
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Erik
Lindahl
Added gbsa
.
itp to Ma
k
efile
.
am in all
amber f
o
rce
fields
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
E
r
ik L
i
ndahl
Changed to n
o
n-prefixed
d
efault
R
NA residue names
i
n
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Erik Linda
h
l
Merg
e
br
a
nch 'master' of git
.
grom
a
cs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-26
E
r
ik Lindahl
C
h
a
n
g
e
d to non-prefixe
d
defau
l
t RNA res
i
due names
in
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Erik L
i
ndahl
Merge branch 'maste
r
'
of gi
t
.
g
r
omacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-26
Erik Lin
d
ahl
Added files i
n
p
r
eparati
o
n
of double-precision AllvsAll
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Eri
k
Lindahl
Ad
d
ed gbsa parameters to
Amber force fields
commit
|
commitdiff
|
tree
2010-07-25
Erik Linda
h
l
Resolved
m
erge conflict
commit
|
commitdiff
|
tree
2010-07-25
Erik Lind
a
hl
Fixed bug
f
or small syst
e
ms in
a
ll-v
s
-all kerne
l
s,
.
.
.
commit
|
commitdiff
|
tree
2010-07-25
Eri
k
Linda
h
l
A
dded DNA/RNA residue trans
l
ati
o
n tables for charmm27
commit
|
commitdiff
|
tree
2010-07-25
E
r
ik Lindahl
En
f
orce rule abou
t
matc
h
ing rt
p
and tdb
names to n
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-07-25
Erik Lindah
l
A
dd
e
d autoconf and cmake checks to make the r
e
strict
.
.
.
commit
|
commitdiff
|
tree
2010-07-25
Er
i
k Linda
h
l
Added a
PO
S
IX/Wi
n
do
w
s portable
way to sc
a
n directo
r
ies
.
.
.
commit
|
commitdiff
|
tree
2010-07-24
E
r
ik Lindahl
Second
b
atch
of file
mo
d
ifications to enable Amber
.
.
.
commit
|
commitdiff
|
tree
2010-07-24
E
rik Lindahl
pdb2g
m
x changes to support
p
rotein/DNA/RNA mixtu
r
es
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
E
rik Lindahl
Remove pro
p
e
r
torsi
o
n
s
with zer
o
forc
e
co
n
stan
t
at
.
.
.
commit
|
commitdiff
|
tree
2010-07-23
Erik
L
indahl
R
e
moved scratch
f
ile
s
from
am
b
e
r
99
commit
|
commitdiff
|
tree
2010-07-21
Eri
k
L
indahl
Fixed bu
g
s that caused type
-
4
i
m
pro
p
e
rs (sam
e
fo
r
m
.
.
.
commit
|
commitdiff
|
tree
2010-07-21
Erik Lindahl
C
h
a
nges t
o
enable Amber99
commit
|
commitdiff
|
tree
2010-06-23
Erik Lin
d
ahl
Added gcc41 check
commit
|
commitdiff
|
tree
2009-12-16
Erik Lindah
l
M
anual application of pa
t
ch 5c076
c
352b4c8a43
b
5
2
ab441691932
e
f
.
.
.
commit
|
commitdiff
|
tree
2009-12-16
Erik Lin
d
ahl
Merge branch
'rele
a
s
e-4-0-patches' of git
.
g
r
omacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2009-12-16
Er
i
k
Lindahl
R
e
moved default nice-19 behavior from md
r
un
e
v
e
n on
.
.
.
commit
|
commitdiff
|
tree
2009-12-12
E
r
i
k Lindahl
R
eplaced acos-based me
t
hod for ca
l
c
ula
t
ing angles between
.
.
.
commit
|
commitdiff
|
tree
2009-12-11
Erik Lindahl
Fixed signed/un
s
igned comp
a
rison
m
ism
a
tch in scanner
.
.
.
commit
|
commitdiff
|
tree
2009-12-11
Er
i
k L
i
nd
a
hl
M
e
rge branc
h
'
m
aster' of git
.
grom
a
c
s
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2009-12-11
Erik Lind
a
hl
F
i
xed err
o
rs in
v
m
dio
.
c
whe
n
c
o
m
p
iled wi
t
h M
S
VC8, 64bit
commit
|
commitdiff
|
tree
2009-12-06
Erik Lindahl
Ve
r
sion bump to 4
.
0
.
7
commit
|
commitdiff
|
tree
2009-12-06
Eri
k
Lindahl
Adde
d
check for 3d
n
ow that was
r
e
m
ov
e
d
w
hen
m
er
g
ing
.
.
.
commit
|
commitdiff
|
tree
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