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Merge "Merge release-4-5-patches into release-4-6" into release-4-6
2012-03-18
Dav
i
d van der Spoel
M
e
rge "Merg
e
rele
a
se-
4
-5-patches into release-4
-
6
"
.
.
.
commit
|
commitdiff
|
tree
2012-03-15
C
h
ristoph Junghans
Mer
g
e "Clarifie
d
w
o
rding of doc
u
men
t
ation" in
t
o release
.
.
.
commit
|
commitdiff
|
tree
2012-03-13
Roland Schul
z
M
erge
"mdr
u
n
-np
m
e without PME or with PD now generate
s
.
.
.
commit
|
commitdiff
|
tree
2012-03-13
Chri
s
to
p
h J
u
n
gh
a
ns
Merge "Vibration spec
t
ra f
r
o
m
velocity ACF or Normal
.
.
.
commit
|
commitdiff
|
tree
2012-03-12
C
h
ristoph J
u
nghans
Mer
g
e "More editorial fixes to tool documentation"
.
.
.
commit
|
commitdiff
|
tree
2012-03-12
Teem
u
Murtola
Merge "Made
d
escription string
for g
_
select -select
.
.
.
commit
|
commitdiff
|
tree
2012-03-09
R
ol
a
nd Schu
l
z
Merge
"Improve F
i
ndF
F
TW"
into release-4-6
commit
|
commitdiff
|
tree
2012-03-09
David van der Spoel
Merge "Improved c
r
yptic error message" in
t
o
r
elease
.
.
.
commit
|
commitdiff
|
tree
2012-03-09
Carsten Kutzn
e
r
Merge "Improve
d
warning note wit
h
DD
a
nd periodic molecu
l
es
.
.
.
commit
|
commitdiff
|
tree
2012-03-08
David van de
r
S
poel
Merge "Minimal
support for Clang" into relea
s
e-4-5
.
.
.
commit
|
commitdiff
|
tree
2012-02-25
D
a
v
id v
a
n
d
er Spoel
Merge "Minor formatting fixes
to
.
mdp
optio
n
doc
u
mentat
i
on
.
.
.
commit
|
commitdiff
|
tree
2012-02-21
Teemu Murtola
Me
r
g
e
"Use Git server
(
m
irror) to avoid fetching problems
.
.
.
commit
|
commitdiff
|
tree
2012-02-21
Christoph J
u
nghans
Me
r
ge "change
d
default
e
psilon-rf value
t
o
0
" into
.
.
.
commit
|
commitdiff
|
tree
2012-02-19
Ber
k
Hess
Merge
"Generate
w
arnings
f
o
r QMMM usage" into
rel
e
as
e
-4-6
commit
|
commitdiff
|
tree
2012-02-15
R
o
land Schu
l
z
M
e
rg
e
"
Cma
k
e:
u
nit
e
FindFFTW3* in
t
o one
f
ile" into
.
.
.
commit
|
commitdiff
|
tree
2012-02-11
Szilárd Páll
Merge
changes If0c2
f
9d9,Ic2a8ad82 i
n
to release-4-5
.
.
.
commit
|
commitdiff
|
tree
2012-02-10
Chr
i
st
o
ph J
u
nghans
Merge
"
F
ixed bug with COM mot
i
on remova
l
on pa
r
t of
.
.
.
commit
|
commitdiff
|
tree
2012-02-08
Ch
r
istoph Junghans
Merge "fixed
c
onf
u
sing nonbonded kernel poin
t
e
r
i
n
itializ
a
ti
.
.
.
commit
|
commitdiff
|
tree
2012-02-03
Dav
i
d v
a
n der Spoel
Merge "Improve
d
t
he a
c
curacy of the sd1 integrator
.
.
.
commit
|
commitdiff
|
tree
2012-02-02
Szilárd Páll
Merg
e
"App
e
nd
al
l
ICC Performa
n
ce flags onl
y
to
Rele
a
s
e
.
.
.
commit
|
commitdiff
|
tree
2012-02-02
Szilárd Páll
Merge "M
e
rges in threading br
a
nch as o
n
e
squashed
co
m
mit
.
.
.
commit
|
commitdiff
|
tree
2012-02-02
Te
e
mu Murtol
a
Merge "Revert "Fix ICC
on
W
ind
o
ws Build"" into release
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
David van der Spoel
Merg
e
"g_sans - tool to com
p
u
te
S
ANS spect
r
a" into
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
David
v
an der Spoel
Merge "Fix
e
d error m
e
ssag
e
to identi
f
y
t
he corre
c
t
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
Dav
i
d van
d
e
r
Spoel
Merge "Fixe
d
trjconv -sub" into rel
e
a
s
e
-
4
-
5
-patches
commit
|
commitdiff
|
tree
2012-02-01
David
van der Spoel
Merge "Impr
o
ved erro
r
messa
g
e" into
release-4-5-patche
s
commit
|
commitdiff
|
tree
2012-02-01
Christo
p
h Junghans
Me
r
ge
"Fix
signed/unsigned wa
r
nings
"
into release-4
.
.
.
commit
|
commitdiff
|
tree
2012-01-31
Roland Schulz
R
e
ve
r
t "F
i
x IC
C
o
n
Windows
Build"
commit
|
commitdiff
|
tree
2012-01-31
David van der
S
poel
Merge "
F
ix ICC on
W
i
ndo
w
s B
u
ild
"
into rel
e
ase
-
4
-
5-patches
commit
|
commitdiff
|
tree
2012-01-31
Mark Abraham
M
e
rge "Corre
c
t
ed use of ?: in
c
onditional" into r
e
leas
e
.
.
.
commit
|
commitdiff
|
tree
2012-01-25
Roland S
c
hulz
Merge "Merge release-
4
-5-patches into
r
elease-4-6"
.
.
.
commit
|
commitdiff
|
tree
2012-01-25
Roland
S
chu
l
z
Merge "New approach
for GerritBuild
s
c
r
ipt" into release
.
.
.
commit
|
commitdiff
|
tree
2012-01-25
Berk
Hess
Merge
"
Added
two
new bo
n
d
ed functions
.
" into
release-4-6
commit
|
commitdiff
|
tree
2012-01-24
S
e
bastian Fritsch
Merge
"
document AdResS md
p
opti
o
n
s" into releas
e
-
4
-6
commit
|
commitdiff
|
tree
2012-01-20
Da
v
id van der Spoel
Merge "Fixed timing measurement
s
.
" int
o
r
elease-
4
-5
.
.
.
commit
|
commitdiff
|
tree
2012-01-18
R
o
land S
c
hulz
R
e
vert
"
R
eplac
e
stderr by stdout i
n
editconf terminal
.
.
.
commit
|
commitdiff
|
tree
2012-01-15
Christo
p
h Jun
g
hans
Merge
"
Added CMa
k
e Toolc
h
ain f
i
le f
o
r BlueGene/P" int
o
.
.
.
commit
|
commitdiff
|
tree
2012-01-14
M
a
rk Abraha
m
Merge "Remove
u
s
e of FindMPI
.
cmake" into rele
a
se-4-6
commit
|
commitdiff
|
tree
2012-01-14
Mark Ab
r
a
h
am
Me
r
ge "Removing outdated vsite
c
omment
"
in
t
o release-4-6
commit
|
commitdiff
|
tree
2012-01-13
Roland Schulz
Merge "Fi
x
ed MSVC compiling with plug-in support" into
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
Christoph Jungh
a
ns
Me
r
g
e
"Docum
e
nted
the funct
i
on of g_cluste
r
-c
l
-
n
oa
v
.
.
.
commit
|
commitdiff
|
tree
2011-12-27
Roland
Schulz
M
erge "Added -dhdl to tpr file list, fixes #8
5
5" into
.
.
.
commit
|
commitdiff
|
tree
2011-12-20
Roland Schulz
Merge "Using MinSizeRel con
f
iguration and Relea
s
e target
.
.
.
commit
|
commitdiff
|
tree
2011-12-20
Rola
n
d Schulz
Mer
g
e changes Iaf4c5
6
b7,Ibabed87f i
n
to r
e
l
ease-4-5
.
.
.
commit
|
commitdiff
|
tree
2011-12-14
Rola
n
d S
c
h
ulz
M
e
rg
e
"Re-
f
ixed stat
i
c linking
of maths li
b
raries
u
n
der
.
.
.
commit
|
commitdiff
|
tree
2011-12-13
Ro
l
a
nd Schulz
Merge "
C
onve
r
ted macro usage for readability" i
n
to
.
.
.
commit
|
commitdiff
|
tree
2011-12-13
Roland S
c
h
u
lz
Merge "Rela
x
ed some assumptions about
t
rajec
t
ory times
.
.
.
commit
|
commitdiff
|
tree
2011-12-11
Roland Schul
z
Merge "Set -DMPI
only if compiled for FAH" i
n
to rel
e
ase
.
.
.
commit
|
commitdiff
|
tree
2011-12-08
Roland Schulz
Merge "Added an option to
e
asily compile contrib progr
a
ms
.
.
.
commit
|
commitdiff
|
tree
2011-12-08
Roland Schulz
Merge "Fix selection pars
i
ng in double pre
c
ision
.
"
.
.
.
commit
|
commitdiff
|
tree
2011-12-08
Rol
a
nd Sch
u
l
z
Merge "Avoid possible warn
i
ngs if HU
G
E
_VAL
!
= infinity
.
.
.
commit
|
commitdiff
|
tree
2011-11-30
Roland
Schulz
Merge "Merge remote-tracking
b
ranch 'gerrit/r
e
lease
.
.
.
commit
|
commitdiff
|
tree
2011-11-27
Roland Schulz
Merge "Fixes inconsistent spelling
o
f Git cma
k
e
variabl
e
s
.
.
.
commit
|
commitdiff
|
tree
2011-11-27
Roland Schu
l
z
Merge "Repla
c
e
'
_' in all mdp options
t
o '-'" into
.
.
.
commit
|
commitdiff
|
tree
2011-11-27
Roland
Schulz
Merge "
C
leaning up some bad
coding practices" into
.
.
.
commit
|
commitdiff
|
tree
2011-11-27
Ro
l
and S
c
h
u
lz
M
e
rg
e
"Initialize variables to
m
ake GCC
4
.
6 not complai
n
.
.
.
commit
|
commitdiff
|
tree
2011-11-27
R
o
land Schulz
Merge
"
Added s
u
ppo
r
t for submission to cdash
s
erv
e
rs
.
.
.
commit
|
commitdiff
|
tree
2011-11-25
Roland Sc
h
ulz
Merge "Changed cryptic
var
i
abl
e
names" into release-4-6
commit
|
commitdiff
|
tree
2011-11-24
Roland S
c
hulz
Merg
e
"Fixed g_a
n
gle
-
f
-or to copy
t
imes from -f to
.
.
.
commit
|
commitdiff
|
tree
2011-11-08
Ch
r
istoph J
u
nghan
s
Mer
g
e "Fixed bug #830 (segv in do_dssp)" into relea
s
e
.
.
.
commit
|
commitdiff
|
tree
2011-11-08
Kasson
Merge "Fix
for
G
B
,
do
u
ble
,
SSE2
a
nd optim
i
zed
kernels
.
.
.
commit
|
commitdiff
|
tree
2011-10-20
Christoph
J
unghans
Merg
e
"Changed defa
u
lt value for
g
_a
n
aeig -last
to
.
.
.
commit
|
commitdiff
|
tree
2011-10-20
Ch
r
i
s
toph
J
u
nghans
Merge
"
Fi
x
e
s for GB kernel" into release-4-5-pat
c
h
es
commit
|
commitdiff
|
tree
2011-10-20
Ch
r
istoph
J
u
nghans
Merge "Ad
d
CMak
e
Li
s
ts
.
txt
.
user to g
i
t
i
gnore" i
n
to release-4-6
commit
|
commitdiff
|
tree
2011-10-19
Teemu Murtola
Merge "fi
x
e
d pull
c
o
n
straining doing
nothing, fi
x
es
.
.
.
commit
|
commitdiff
|
tree
2011-10-15
Christo
p
h Ju
n
g
h
ans
Merge "Fixes MPI_
G
R
O
UP_EMPTY for tMPI" i
n
to release-4-6
commit
|
commitdiff
|
tree
2011-10-06
Szilárd
Páll
Merge "Remo
v
ed dupl
i
cate CMa
k
e
functionality" int
o
.
.
.
commit
|
commitdiff
|
tree
2011-09-27
Rosse
n
Apos
t
olov
M
er
g
e
"Removed CMake wa
r
ni
n
g for recent OpenMPI
versions
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
Rossen Apostolov
Merge "Resolved gerrit issue https://gerrit
.
gro
m
acs
.
.
.
commit
|
commitdiff
|
tree
2011-09-16
Rossen
A
postolov
Merge
"
g_wha
m
: fixed pullx
.
xv
g
reading
issue with pul
l
_geo
m
e
.
.
.
commit
|
commitdiff
|
tree
2011-09-16
Erik Lindahl
Merge "
m
ade all
o
cation for LINCS with
p
article decomposition
.
.
.
commit
|
commitdiff
|
tree
2011-09-15
B
e
rk Hess
Me
r
ge "Introduced
d
iffer
e
nt opti
o
ns for pdb2gm
x
te
r
min
i
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Ros
s
e
n A
p
osto
l
ov
Merge
"
Added warning line
.
" into rele
a
s
e
-4-5
-
patches
commit
|
commitdiff
|
tree
2011-09-13
Berk Hess
M
e
rge "Fix pdb2gmx -de
b
ug and
.
hdb
files" into release
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Berk Hess
Merge
"
F
ixed charge groups of
C
HARMM27 DNA
/
R
N
A terminal
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Berk Hess
Mer
g
e "Added ACE and CT3 t
o
CHARMM27 am
i
no
a
cids
.
rtp
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
R
o
l
a
n
d Schulz
Me
r
ge "f
i
xed g
r
ompp issue w
i
th decoupling a
n
d virtua
l
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
R
o
ssen Apostolov
Mer
g
e
"
Fi
x
es for C
M
ak
e
f
i
nding FORTRAN library names
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Berk Hess
Merge "Remove
segv in xpm2
p
s, fixes #
6
1
1" int
o
release
.
.
.
commit
|
commitdiff
|
tree
2011-09-05
Michael
Shirts
Merge
"fi
x
ed incorrect
p
V
term in the energy file"
.
.
.
commit
|
commitdiff
|
tree
2011-08-23
R
o
land Sch
u
lz
Merge "
F
ixed g_disre de
r
efe
r
e
n
cing cr" int
o
re
l
ease
.
.
.
commit
|
commitdiff
|
tree
2011-08-23
Roland Schulz
Merge "Typo fix" into
r
elease-4-
5
-pa
t
ches
commit
|
commitdiff
|
tree
2011-08-23
R
o
l
and Sch
u
lz
Merge
"
fixed
operation
o
n cl
o
sed file struc
t
u
r
e in
.
.
.
commit
|
commitdiff
|
tree
2011-08-23
Roland Schulz
Mer
g
e "
f
ixed possible i
n
fini
t
e lo
o
p
w
h
e
n reading atom
.
.
.
commit
|
commitdiff
|
tree
2011-08-11
Roland
S
chulz
Merge "remo
v
ed npmenodes m
i
smatch warn
i
ng
i
n r
e
ad_checkpoint
.
.
.
commit
|
commitdiff
|
tree
2011-08-11
Berk Hess
Merge "Make sure that ftell works correctly for files
.
.
.
commit
|
commitdiff
|
tree