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Fixed incorrection AmberGS force field (redmine #728)
2011-09-13
E
rik Li
n
dahl
F
i
x
e
d i
n
c
o
rrec
t
ion Amb
e
rGS
force f
i
e
ld (re
d
mine
#728)
commit
|
commitdiff
|
tree
2011-05-05
Erik Lindahl
Merge branch '
r
e
lease-4-5-patches'
o
f git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-05-05
Erik
L
ind
a
hl
Update doc to clari
f
y that Amber nucleic params are
.
.
.
commit
|
commitdiff
|
tree
2011-01-30
Erik Lindahl
Impro
v
ed PBC handling f
o
r large molecul
e
s duri
n
g
cluster PBC
commit
|
commitdiff
|
tree
2011-01-30
Erik
Lindah
l
Fixed
t
he pbc cluster o
p
t
i
on
o
f trjconv by sw
i
tching
.
.
.
commit
|
commitdiff
|
tree
2010-10-09
Erik Lindahl
Merge b
r
anch 're
l
e
a
s
e
-4-5-patches'
o
f
g
it
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-10-09
Erik Lindahl
Fixe
d
unin
i
tialized va
r
iable warn
i
ng in grompp
.
c
commit
|
commitdiff
|
tree
2010-09-01
Erik Lindahl
Remov
e
d lots
o
f unnece
s
s
ary mes
s
ages to s
t
dout
from
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
E
r
ik Linda
h
l
Ad
d
ed Gerrit to the l
i
st
o
f autho
r
s
.
So
r
ry
for
f
org
e
tting
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Ma
d
e
the
o
ptions program for
t
h
e
l
atex manual com
p
ile
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Er
i
k Li
n
d
a
hl
Fixed
t
y
po in src/
c
o
n
trib/
M
akefile
.
am
commit
|
commitdiff
|
tree
2010-08-31
E
r
i
k
L
in
d
ahl
Fixe
d
incorrec
t
c
a
ll to gmx_f
i
nalize() in gmx
_
p
m
e_error()
commit
|
commitdiff
|
tree
2010-08-31
E
rik Lindahl
Added final
n
ewline
t
o avoid co
m
piler war
n
ing
i
n sfactor
.
h
commit
|
commitdiff
|
tree
2010-08-31
E
r
ik Lind
a
hl
Mer
g
e branch 'relea
s
e-
4
-5-patches' of git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik
Li
n
dahl
Ad
d
e
d
C
p
ack support
commit
|
commitdiff
|
tree
2010-08-31
Er
i
k Lindahl
Ad
d
ed label writing capabil
i
ty to
edi
t
conf
w
hen used
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Ad
d
ed check
f
o
r
<2 frames whe
n
autocorrelati
o
n is reques
t
ed
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Eri
k
Lin
d
ahl
Mov
e
d buggy a
n
d un
s
upported g_sdf to co
n
trib directory
.
.
.
commit
|
commitdiff
|
tree
2010-08-30
Erik Lindahl
Impro
v
ed handling of
i
nc
l
ude
p
aths
i
n
gmxcpp
f
ro
m
Tee
m
u
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik Lindahl
Added longer list
o
f aut
h
ors
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k Lind
a
hl
Merge br
a
nch 'rel
e
ase-4-5-patches' of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
i
k
Lindahl
Added check
f
or SS
E
2 support to use generalized born
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Added tr
j
c
onv che
c
k for topol
o
gy
p
rescence, see bugzilla 526
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindah
l
Merge b
r
anch 'release-4-5-patches' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
F
ix
e
d gmxcpp to always use unix path
s
eparators in
.
.
.
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
F
i
xed anot
h
er uninitialized variabl
e
warning in gmx_energy
.
c
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k Lindahl
Add
curr
e
n
t
path (
.
/) t
o
topol
.
top include when force
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik L
i
ndahl
Don
t
write EOF
warnin
g
s to stdout ev
e
ry time we checkpoint
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
Li
n
dahl
Merge
bra
n
ch 'release-4
-
5-patches' of
git
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lind
a
hl
Fixed first s
t
atemement
o
cc
u
r
ing
b
efor
e
variable de
c
laration
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Merge b
r
anch 'relea
s
e-4-5-patches' of git
.
gr
o
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Modified p
d
b2gmx to automatical
l
y
p
i
ck the force field
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik Lind
a
hl
Fi
x
ed
p
ointer typ
o
in
patch from A
l
e
xey
Shvetsov
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
Lindahl
Added PBC checking patch to g_cluster
f
r
om
Alexey Shvetsov
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Merg
e
branch 'r
e
lea
s
e-4-5-patches' of git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
M
odified pdb2g
m
x to not
a
cce
p
t extra hydrogen atoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k
L
ind
a
hl
Merge
b
r
anch 'release-
4
-5-pa
t
c
h
es' of
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
true/fals
e
in
p
ut
s
ettings
s
hould be called b
o
ol instead
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
M
e
rge branch
'
release-
4
-5
-
patc
h
es
'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Revert "Made pdb2g
m
x be
slightly more he
l
pful when
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
ri
k
L
i
nda
h
l
Upd
a
t
ed com
p
letions for 4
.
5 re
l
ease
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Made /usr/local/
g
romacs
d
e
faul
t
installation path in
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k Lindahl
Updated html do
c
u
mentation for
r
e
l
eas
e
4
.
5
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k Lindahl
Updated
m
an
u
al pages, now with correct versi
o
n (4
.
5
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
F
ix for warning
in ngmx mak
e
file
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k
L
indahl
Ch
a
nged
version to b
e
ta4
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
U
pdat
e
d scripts
to
p
roduce 4
.
5
ma
n
p
a
g
e
s
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Updated man
p
ages for 4
.
5 release
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindah
l
Removed useless g_lo
g
o and g_highway programs from
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k
Lin
d
ahl
g_
k
inetics removed
f
rom automa
t
i
c
ally built p
r
ograms
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Fixed include
p
ath in vmdio
.
h
commit
|
commitdiff
|
tree
2010-08-25
E
r
ik
Lindahl
Fo
r
got to actually do the
cha
r
->
i
nt change
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Lindahl
Cha
n
ged bool to signed
integer inste
a
d of
u
n
s
ig
n
ed
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik
L
indah
l
Add
e
d missing header include
commit
|
commitdiff
|
tree
2010-08-25
E
rik Lind
a
hl
Merge b
r
anch 'releas
e
-
4-5-patc
h
es' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
Erik Linda
h
l
Made
sure all source file
s
ha
v
e s
o
me copyr
i
ght hea
d
er
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik
L
indahl
Re-adde
d
openmm pap
e
r
commit
|
commitdiff
|
tree
2010-08-24
Erik Lin
d
ahl
Merge branch 'rele
a
se-
4
-5-
p
atches' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-24
Erik
Lind
a
h
l
U
pdated intel
syntax x86-6
4
asm files to also support
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
h
l
Fixed uninitiali
z
ed
v
ariab
l
e error in
G
B
k
ernel wit
h
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
F
ixed an
unsigned/s
i
gned i
n
teger comparison
commit
|
commitdiff
|
tree
2010-08-22
Erik Lind
a
hl
Fixed
t
wo more i
n
stances of strcasecmp->gm
x
_strcasecmp
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindahl
Copie
d
SSE int
r
insi
c
s kern
e
ls from x86-64 t
o
ia
3
2
commit
|
commitdiff
|
tree
2010-08-22
Erik
L
indahl
R
e
plac
e
d
all occurences of str(
n
)casecmp
w
i
th gmx
_
str
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lindah
l
Fixed
stu
p
id mistake w
h
ere a state
m
e
nt was placed before
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
E
rik Li
n
dahl
Replaced testin
g
of git versi
o
n wit
h
t
e
s
t
i
ng for fe
a
tures
commit
|
commitdiff
|
tree
2010-08-22
E
r
ik Lindahl
Fixed naming
problems for double precis
i
on Fortran
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Lindah
l
Fi
x
ed a typo in
futil
.
h
commit
|
commitdiff
|
tree
2010-08-22
Er
i
k L
i
ndahl
M
e
rge branch 'release-4-5-patches' of
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Linda
h
l
Clean
e
d
up
all installed hea
d
ers to re
m
ove strict dependenc
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik Li
n
dahl
Removed
s
ome u
n
nece
s
sa
r
y
#if
d
efs from str
i
n
g
2
.
h
;
all
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
Erik
Lin
d
ahl
Amber fo
r
ce field
s
n
ow pass va
l
idation
.
Beta stat
u
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Eri
k
Lindahl
Added F77 kernel
s
etup headers
commit
|
commitdiff
|
tree
2010-08-21
E
rik
L
ind
a
hl
Fix
e
d s
y
nchroniz
a
t
ion counter update for f77 k
e
rne
l
s
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Fixed a
b
ug for GB
OB
C
born
r
adiu
s
calcul
a
tion in SSE
2
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Li
n
dahl
F
i
x
ed
a
n
uninitializ
e
d var
i
able b
u
g
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
F
ixed
a
minor bu
g
tha
t
c
aus
e
d Fo
r
tran builds to fa
i
l
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Don
t
write
n
o
n
po
l
a
r
s
urfa
c
e energy to en
e
rgy fi
l
e if
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
E
rik Linda
h
l
Fixed so Fortran kernels work again
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindah
l
U
p
g
r
aded
t
o latest
a
u
t
oconf platfo
r
m
d
etection sc
r
i
pts
commit
|
commitdiff
|
tree
2010-08-21
E
rik Li
n
dahl
Fixed a chain rule error in doub
l
e
p
r
ec
.
SSE2 GB for
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik Lindahl
Merg
e
bran
c
h
'r
e
lease-4
-
5-patches' of git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-21
Erik
L
indahl
Double p
r
ecision
SSE2 ker
n
els f
o
r Gener
a
lize
d
Born
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Linda
h
l
Upd
a
ted GB SSE2
ke
r
nels, testing in pro
g
r
ess now
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
i
ndahl
Merg
e
b
ran
c
h
'
release-4-5-patches' of git
.
g
r
omacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
Lindahl
Modifie
d
at
o
m order
in A
m
be
r
nu
c
leotide im
p
r
oper torsions
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
Lindahl
M
o
dified impro
p
er torsion atom order
i
n A
m
ber TRP re
s
idues
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Er
i
k Lindahl
Merge branch
'
release-4-5-patches' of gi
t
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindahl
Fix to
w
rite GB and sur
f
ace ener
g
y to sepa
r
ate ter
m
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik
L
indahl
Merge branch 'r
e
l
ease-4-5-
p
atches'
o
f git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
E
r
ik Lin
d
a
h
l
Enabled dou
b
le precision all
-
vs-all ke
r
ne
l
s
.
Tested
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Erik Lind
a
hl
Fixed simple typo i
n
l
ast commit
commit
|
commitdiff
|
tree
2010-08-18
Erik Lindah
l
F
ix
e
d previous n
a
s
m-s
e
g
v
bug
f
or inte
l
-syntax
S
S
E
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Fixed 64-bit
bug in SSE ass
e
mbly (only visible with
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik Lindahl
Wo
r
ked around an i
n
t
ernal compiler err
o
r f
o
r MSVC when
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Er
i
k
L
ind
a
hl
Merge branch
'releas
e
-
4-5-patches' of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
E
rik Li
n
dahl
Deprecated -ins option to g_hbond since nobod
y
seems
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Erik
Lindahl
C
o
pied
a
ll-vs-a
l
l change from x86-64 to ia32 kernel
s
to
o
commit
|
commitdiff
|
tree
2010-08-17
E
rik Lindahl
Merge branch 'rel
e
ase-4-
5
-patches' of
g
it
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
next