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Added label writing capability to editconf when used with an index file
2010-08-31
Erik Lin
d
ahl
Added label writing capability to edi
t
c
o
nf
when
u
s
ed
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Adde
d
check for <2 f
r
ames
when a
u
tocorrelation is request
e
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Move
d
buggy and
u
ns
u
p
ported g_sd
f
to c
o
ntrib direc
t
ory
.
.
.
commit
|
commitdiff
|
tree
2010-08-30
Erik Lindahl
Improved han
d
ling
of include paths in
gmxcpp
f
rom
T
eemu
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
A
d
ded lo
n
g
e
r
l
ist of auth
o
rs
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Merge branch 'release
-
4-5-patc
h
e
s
' of
g
it
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Added check for
S
S
E2 support to use generalized bo
r
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
A
dded
t
rjconv chec
k
for topology p
r
esc
e
n
ce, s
e
e bug
z
illa 526
commit
|
commitdiff
|
tree
2010-08-27
Erik
L
i
ndahl
M
e
rge branch 'release-4-5
-
patc
h
e
s
' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lin
d
ahl
Fixed gmxcpp
to a
l
ways u
s
e unix pa
t
h separ
a
tors in
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
Lindahl
Merge
branch 'rele
a
se-4-5-pa
t
c
h
es
'
o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lin
d
ahl
Fix
e
d ano
t
her uninitialized varia
b
le warning in gmx_en
e
rgy
.
c
commit
|
commitdiff
|
tree
2010-08-27
Erik Lin
d
a
hl
Add c
u
r
r
ent path (
.
/)
t
o topol
.
top include when force
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Dont wri
t
e
E
OF wa
r
nings to stdout every ti
m
e we checkpoint
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
M
erge branch 'release
-
4-5-patches' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Fixed fir
s
t
statemement occuring before variable declaration
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Merge b
r
anch 'release-4-5-pat
c
hes' of git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
L
i
ndahl
M
o
dified pdb2
g
mx to automatically pic
k
the force
fie
l
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Li
n
dahl
Fixed po
i
nter typo
i
n
patch fr
o
m Alexey Shvet
s
ov
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
A
d
d
e
d
P
B
C
checki
n
g patch to g_cluster
f
rom Alexey Shvetsov
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Merge
b
ranch '
r
elease-4-5-pat
c
hes' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Modif
i
ed pdb2
g
mx t
o
not accep
t
extra hydro
g
en atoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik L
i
ndahl
Merge branch 'r
e
l
eas
e
-4-5-p
a
tch
e
s' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
rik Lindahl
t
r
u
e
/false input
setting
s
should be
cal
l
ed boo
l
instead
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
M
erge br
a
nch 'release-
4
-5-patches'
o
f
gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Li
n
d
a
hl
Revert "Made
p
db2gm
x
b
e slightly more he
l
pfu
l
when
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Updated complet
i
ons for
4
.
5
r
e
l
e
a
se
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Made /usr/local/gromacs default installation pa
t
h
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Upda
t
ed html d
o
cu
m
entation
f
or rel
e
ase 4
.
5
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Up
d
ated manual pages, now w
i
th correc
t
versi
o
n (
4
.
5
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Fi
x
for war
n
ing in ngmx makefile
commit
|
commitdiff
|
tree
2010-08-26
Erik Lin
d
ahl
Chang
e
d version
t
o beta4
commit
|
commitdiff
|
tree
2010-08-26
E
rik Lindahl
Up
d
ated
sc
r
i
p
ts to
produce 4
.
5
ma
n
p
age
s
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k
L
i
nd
a
hl
Updated manpages for 4
.
5 releas
e
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
Lindahl
Removed useless g_logo
an
d
g
_highwa
y
p
r
ogra
m
s
from
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k L
i
ndahl
g_kinetics r
e
mo
v
ed
from automatically built programs
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik
Lindahl
F
ixed include path in vmdio
.
h
commit
|
commitdiff
|
tree
2010-08-25
Er
i
k L
i
ndahl
F
o
rgot to actu
a
lly do the cha
r
->int chang
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Change
d
bool to sign
e
d int
e
ger instead o
f
unsigned
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Li
n
da
h
l
Added missing heade
r
incl
u
de
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Merge
branch
'release-4-5-patches' of
g
it
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
E
r
i
k
Lindahl
M
ade
s
ure all
source files have
s
ome copyright he
a
der
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik Lindahl
Re-
a
d
d
ed openmm
p
aper
commit
|
commitdiff
|
tree
2010-08-24
Erik Lindahl
M
e
rge branch 'release-4-5-patches'
o
f git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik Li
n
dahl
U
pdated intel s
y
ntax x86-64 a
s
m files to also su
p
port
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik Li
n
dahl
Fixed uni
n
i
t
ializ
e
d va
r
iabl
e
error in
G
B kernel with
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik
Linda
h
l
Fixed an unsi
g
ned/signed integer compa
r
ison
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fixed
t
wo m
o
re
i
nstances
o
f strcasecmp->gmx_
s
trcasecmp
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindah
l
Copied SSE
i
ntrins
i
c
s
kernel
s
f
r
o
m x86-64 to ia32
commit
|
commitdiff
|
tree
2010-08-22
Erik Li
n
dahl
Re
p
l
a
ced all occure
n
ces of str
(
n
)
c
asecmp with gmx_str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Fix
e
d
s
t
upid mistake w
h
ere a statement was placed
before
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lindahl
Replaced testi
n
g of
g
it ver
s
ion with testing f
o
r featur
e
s
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
Lind
a
h
l
Fix
e
d
nam
i
ng probl
e
m
s
for
d
ouble precision For
t
ran
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik
L
ind
a
hl
Fixed a typ
o
in futil
.
h
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Merge br
a
n
c
h 'release-4-5-patches' of
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
Lindah
l
Cl
e
aned up all
i
nstalle
d
heade
r
s to remov
e
strict dependence
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
L
indahl
R
e
move
d
some u
n
n
e
cessary #ifdefs from str
i
ng2
.
h;
a
ll
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Eri
k
L
i
ndahl
Amber force fields n
o
w
p
a
ss validation
.
Beta
s
tatus
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Ad
d
e
d F7
7
ker
n
el setup hea
d
ers
commit
|
commitdiff
|
tree
2010-08-21
Erik Lin
d
a
hl
Fixed synchronizatio
n
co
u
nt
e
r u
p
date for f
7
7
k
e
rnels
commit
|
commitdiff
|
tree
2010-08-21
E
rik
L
indahl
Fixed a bug for GB OBC born radius calculation
i
n SSE2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k L
i
nd
a
hl
Fix
e
d
a
n uninitialized variable bug
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k Lindahl
Fixed a m
i
n
o
r bug that caused Fortran builds to f
a
i
l
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k
L
indahl
Don
t
w
r
ite nonpolar surface energy
t
o energy fil
e
i
f
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k Linda
h
l
Fixe
d
so Fortran kerne
l
s work again
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Upgrad
e
d to
lates
t
autoconf
p
latform detection scripts
commit
|
commitdiff
|
tree
2010-08-21
Er
i
k Lindahl
Fixed a chain rule error in
double prec
.
SSE2 GB for
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
M
erge branch 'r
e
lease
-
4-5-pat
c
hes' of g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lin
d
ahl
D
o
u
b
l
e
pr
e
cision SSE2 k
e
rnels for Generalized Bor
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Updat
e
d GB SSE2 k
e
rnels,
testing in p
r
og
r
ess
now
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik L
i
ndahl
Me
r
ge branch 'release-4-
5
-patches'
of
g
i
t
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
indahl
Modi
f
ie
d
a
t
om o
r
d
e
r
i
n Amber n
u
cleo
t
id
e
im
p
roper
t
o
r
sions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
M
o
dified im
p
roper torsion a
t
om order in
Ambe
r
TRP residues
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Er
i
k
Linda
h
l
M
e
rge
bra
n
ch
'
release-
4
-5-patch
e
s
' of git
.
g
r
om
a
cs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Eri
k
Lindahl
Fix t
o
write
G
B and surf
a
ce en
e
rgy to separate
t
erms
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Merge branch
'
rele
a
se-4-5
-
p
a
tches' of
git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
indahl
Enabl
e
d double prec
i
sion al
l
-vs
-
a
l
l
k
er
n
els
.
Tested
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Fixed simple typo in last
c
o
m
mit
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Fixed previous nasm
-
segv bug for
i
ntel
-
s
yntax SSE in
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Linda
h
l
F
i
xed 64-bi
t
bug
i
n SSE
ass
e
mbly (only
vi
s
ible with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Er
i
k L
i
ndahl
Worked ar
o
und an inte
r
n
a
l comp
i
le
r
err
o
r f
o
r
MSVC when
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Merge
b
ranc
h
'rele
a
se-4-5-patc
h
es' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik L
i
n
da
h
l
D
e
p
r
ecated -
i
ns option to g_hbon
d
s
i
n
ce nobody s
e
ems
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
L
indahl
Copie
d
a
l
l-vs-all change fr
o
m
x
86-
6
4
to ia32 kernels too
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Merge b
r
anch 'releas
e
-4-
5
-pa
t
ches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Fi
x
ed potential
error in coulomb ene
r
g
y
, and maybe
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Er
i
k Lindahl
Me
r
ge
br
a
n
ch 'release-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lin
d
ahl
Add
e
d d
o
uble
p
recis
i
o
n
S
S
E2 gene
r
alized born kernels
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
rik
Lind
a
hl
Added ia32 all-
v
s-all kernel
s
commit
|
commitdiff
|
tree
2010-08-12
Erik L
i
ndahl
Updated auto
c
onf to wo
r
k
with renamed SSE2 x86-64 as
m
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Re
n
amed SSE2
x
86-64 asm tes
t
f
i
le to be consistent
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik
L
indahl
F
ixed typo to
d
e
tect both x
8
6
_
64->i386 and
i
3
86->x86_64
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Merge
branch
'release-4-5-patches' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixed a naming erro
r
introduced ye
s
terd
a
y
in 32bit
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lindahl
Fixe
d
compiler
errors for MSVC inline
intrinsics a
n
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
E
r
ik Li
n
dahl
Fixed checkpoint pro
b
lem in 32 bi
t
s
.
We shou
l
d always
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Er
i
k Lindahl
Removed extra TER rec
o
r
d
s
aft
e
r cha
i
ns we think are
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Erik Lind
a
hl
Merge bran
c
h
'release-4-
5
-patc
h
es'
of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Er
i
k Lindahl
Fixed SSE kernels
i
n
d
ouble precision for Cmak
e
,
working
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Er
i
k
L
i
ndahl
M
erge branch 'release-4-5-patc
h
es' of gi
t
.
groma
c
s
.
or
g
.
.
.
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