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Merge "Some changes for md-vv extracted from 4.6" into release-4-5-patches
2013-04-19
Mark
A
braham
Merge "Some changes for md-
v
v extracte
d
from 4
.
6" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
Merge "Fix trjconv
-sub with
.
trr files" i
n
to rele
a
se
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland Schulz
Merge "Added check for vali
d
wa
l
l_a
t
o
m
t
y
pe i
n
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abraham
F
ix trjconv -sub with
.
trr files
commit
|
commitdiff
|
tree
2013-01-15
C
hristoph Ju
n
ghans
Merge
"
Added fata
l
err
o
r for con
s
traints + L
-
BFGS mi
n
imizer
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Mark Abra
h
am
Veloci
t
y-verlet integrators and
v
-rescale are br
o
ken
commit
|
commitdiff
|
tree
2013-01-14
David v
a
n
d
er Spoel
M
erge "Fixing
trjconv -sub" int
o
release-4-
5
-patches
commit
|
commitdiff
|
tree
2013-01-14
David van d
e
r
Spoel
Merge "Noting th
a
t
and why gmxdump -s
-
sy
s
is br
o
ken
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Rol
a
nd
S
c
hulz
M
erge
"Print
out atom numbers in
g
_rmsf" in
t
o release
.
.
.
commit
|
commitdiff
|
tree
2012-11-26
Eri
k
Linda
h
l
M
erge
"
Use st
a
t
for gmx_is_file
.
F
i
x get_
l
ibdi
r
with
.
.
.
commit
|
commitdiff
|
tree
2012-11-20
Christoph Jungh
a
ns
Merge "Fixes bug in g_hbond that
m
ake
s
it produce fatal
.
.
.
commit
|
commitdiff
|
tree
2012-10-27
Chr
i
s
t
oph Ju
n
ghans
Merge
"Fix la
r
ge file support" into rel
e
ase-4-5-patches
commit
|
commitdiff
|
tree
2012-10-26
D
a
vid v
a
n der Spo
e
l
Merg
e
"Fixed Pulp
Fiction q
u
ote" into re
l
eas
e
-4-5
-
patches
commit
|
commitdiff
|
tree
2012-10-08
Manuel Luitz
P
r
int
o
ut atom n
u
m
b
ers i
n
g_rmsf
commit
|
commitdiff
|
tree
2012-09-27
Christoph Jung
h
ans
Merge "Fixed a
n
o
ff-
b
y-o
n
e
error in atom counti
n
g in
.
.
.
commit
|
commitdiff
|
tree
2012-09-27
Tee
m
u
Murtola
Mer
g
e "Fix
insolidang
l
e selections near poles
.
" into
.
.
.
commit
|
commitdiff
|
tree
2012-09-25
Christoph Jung
h
a
ns
Merge "Fix
REMD u
s
e of
g
mx_large_int_t for #steps variable
.
.
.
commit
|
commitdiff
|
tree
2012-09-15
Ka
s
son
Merge "Fix some memory l
e
aks
.
" in
t
o
release-4-5-patc
h
es
commit
|
commitdiff
|
tree
2012-09-15
Dav
i
d van
d
er Spoe
l
Merge "Adapted NMR related dat
a
to
new
pdb fo
r
mat
.
.
.
.
commit
|
commitdiff
|
tree
2012-09-14
Christo
p
h
Ju
n
gh
a
ns
Merge
"
fi
x
ed
r
ecent bug with gromp
p
check for P
-
R P
.
.
.
commit
|
commitdiff
|
tree
2012-09-06
R
o
l
and Schulz
Mer
g
e "Fixed
.
g96
t
rajectory read
i
ng
.
"
into releas
e
.
.
.
commit
|
commitdiff
|
tree
2012-09-03
K
asson
Me
r
ge "Document correct c
o
mm_mode option" into release
.
.
.
commit
|
commitdiff
|
tree
2012-09-03
Kasson
Merg
e
"Impr
o
ved pdb2
g
m
x outp
u
t
" into release
-
4-5
-
p
a
tc
h
es
commit
|
commitdiff
|
tree
2012-08-20
C
h
ristoph Junghans
M
erge "
F
ix coo
r
d
i
n
ate
i
s
z
ero check in g
m
x
check" into
.
.
.
commit
|
commitdiff
|
tree
2012-08-07
C
h
ristoph Junghans
Merge "fixed incorrect T
P
I re
s
u
lts with dynamic box
.
.
.
commit
|
commitdiff
|
tree
2012-08-06
Christoph Junghans
Merge "Added comment in get_structure about w
h
i
ch structures
.
.
.
commit
|
commitdiff
|
tree
2012-08-04
Ro
l
and Schulz
Merge "Fixed
segv in essent
i
al dyna
m
i
c
s mod
u
le" into
.
.
.
commit
|
commitdiff
|
tree
2012-07-09
Christo
p
h
J
ungh
a
ns
M
erge "Fixe
d
bug
in sfacto
r
.
c tha
t
makes g_rdf -s
q
.
.
.
commit
|
commitdiff
|
tree
2012-06-19
Mark Abr
a
ham
Me
r
ge "Fixes #882
- loo
p
ing bug in trxio
.
c" into
r
e
leas
e
.
.
.
commit
|
commitdiff
|
tree
2012-06-19
Chr
i
stoph Junghans
Merge "Quie
t
l
inker on BlueG
e
ne"
into
release-4
-
5-patches
commit
|
commitdiff
|
tree
2012-06-18
Christ
o
ph
Ju
n
gh
a
n
s
Merge "Fix g_lie counting last fra
m
e t
w
ice" into release
.
.
.
commit
|
commitdiff
|
tree
2012-06-16
David van d
e
r Spoel
Fixes
#
882 - looping bug in trxio
.
c
commit
|
commitdiff
|
tree
2012-06-15
Erik M
a
rklund
Ma
k
es
g_hbond -contact work
commit
|
commitdiff
|
tree
2012-06-15
Chr
i
stoph Jun
g
h
a
ns
M
e
rge
"
Wo
r
k around failure of
e
n
dianness
t
es
t
ing on
.
.
.
commit
|
commitdiff
|
tree
2012-06-14
R
oland Schu
l
z
M
erge "Made mdrun mor
e
ver
b
ose about PME split" into
.
.
.
commit
|
commitdiff
|
tree
2012-06-11
Car
s
ten Kutzner
Small fix f
o
r g_tune_pme
commit
|
commitdiff
|
tree
2012-06-08
Chris
t
oph
Jungh
a
ns
Mer
g
e "Added more su
g
gested
s
trat
e
gies to error message
.
.
.
commit
|
commitdiff
|
tree
2012-06-01
Christo
p
h Jungha
n
s
Merge "Replace our ff
t
pack
v
ersion
w
ith Numpy'
s
v
ersion
.
.
.
commit
|
commitdiff
|
tree
2012-05-29
Sander Pronk
R
emoved dep
e
ndency
o
n w
i
ndows
.
h through commre
c
.
h
,
.
.
.
commit
|
commitdiff
|
tree
2012-05-28
Christoph
J
ung
h
a
n
s
Merge "Continuing to fix thread
i
ng on
Cygw
i
n" into
.
.
.
commit
|
commitdiff
|
tree
2012-04-28
Ma
r
k Abraham
M
e
r
ge
"Remove c
h
ecks
b
ased on Generator
"
int
o
rele
a
s
e
.
.
.
commit
|
commitdiff
|
tree
2012-04-28
Mark A
b
raham
Merge "Fix version
in
f
o
g
eneration fo
r
auto
c
onf
.
"
i
nto
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
Sz
i
lárd Páll
Me
r
ge "fixed initial COM motion removal with m
u
ltiple
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
David van
der Spoel
M
erge "Various improvem
e
nts t
o
sh
e
ll code" into release
.
.
.
commit
|
commitdiff
|
tree
2012-04-24
Berk Hess
Merge "allow -
a
ppend to overrule unsupported
fi
l
e lock
i
ng
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
Sa
n
der Pronk
Merge "
P
ermi
t
t
h
reads build o
n
Cygwin" into rele
a
se
.
.
.
commit
|
commitdiff
|
tree
2012-04-14
T
e
emu Murtola
Merge "Clarified warning message" into releas
e
-4-5
.
.
.
commit
|
commitdiff
|
tree
2012-04-14
Teem
u
Murtola
Mer
g
e "Clar
i
fied wa
r
nin
g
string" into release-4-5-pa
t
ches
commit
|
commitdiff
|
tree
2012-04-09
Christo
p
h
Junghans
Merge "Docum
e
n
t
ati
o
n
an
d
e
r
ror message enhanceme
n
ts
.
.
.
commit
|
commitdiff
|
tree
2012-04-09
Christoph Junghans
Merge
"
Cons
o
lid
a
ted
d
ocumentat
i
o
n of
.
mdp
r
estrai
n
t
.
.
.
commit
|
commitdiff
|
tree
2012-04-03
Rola
n
d S
c
hulz
M
e
r
ge
"
Fixes probl
e
ms w
i
th g_msd
and g_energy" in
t
o
.
.
.
commit
|
commitdiff
|
tree
2012-04-02
Da
v
id
van der Spoel
M
e
rge "Improved pdb2gmx error me
s
s
a
ge" into release
.
.
.
commit
|
commitdiff
|
tree
2012-03-18
Christoph Jun
g
han
s
M
erge "W
a
rnings against equilibrating
with P-R P-coupling
.
.
.
commit
|
commitdiff
|
tree
2012-03-18
David van
der Spoel
M
e
rge "Fix typo in C
l
ang CFlags" into r
e
lease-4-5-pa
t
ches
commit
|
commitdiff
|
tree
2012-03-15
Christoph Junghans
Merge
"
Clar
i
fied wording
of documentatio
n
" into releas
e
.
.
.
commit
|
commitdiff
|
tree
2012-03-12
Chr
i
stoph Jun
g
h
a
ns
Merge "More editori
a
l fixes to
tool
documentation"
.
.
.
commit
|
commitdiff
|
tree
2012-03-12
Teemu Murtola
Merg
e
"Made description
s
tring
for g_select -sele
c
t
.
.
.
commit
|
commitdiff
|
tree
2012-03-09
D
a
vid
van der Spo
e
l
Mer
g
e
"Improved crypt
i
c
err
o
r
messag
e
" into
r
e
leas
e
.
.
.
commit
|
commitdiff
|
tree
2012-03-09
Carsten Kut
z
ner
Merge "Impr
o
ved warning
note with
DD and
p
e
riodic molecules
.
.
.
commit
|
commitdiff
|
tree
2012-03-08
Da
v
id van der Spoel
M
e
r
ge "Minimal
s
upport
f
or
Cla
n
g" into
r
e
le
a
se-4-5
.
.
.
commit
|
commitdiff
|
tree
2012-02-25
David van der Spoel
Merge "Mino
r
f
o
r
m
a
t
ti
n
g f
i
xes
to
.
m
dp option documentatio
n
.
.
.
commit
|
commitdiff
|
tree
2012-02-21
Te
e
mu M
u
rtola
Merge "Use Gi
t
serve
r
(mirror) to a
v
o
i
d
fetc
h
ing problems
.
.
.
commit
|
commitdiff
|
tree
2012-02-11
Szilárd
P
áll
Merge changes If
0
c2
f
9d9,Ic2a8ad82 i
n
to r
e
lease-
4
-5
.
.
.
commit
|
commitdiff
|
tree
2012-02-10
Chr
i
stoph Ju
n
g
h
ans
Merge "Fixed
b
u
g with COM motion
r
emova
l
on p
a
rt
of
.
.
.
commit
|
commitdiff
|
tree
2012-02-02
Szilár
d
Páll
Merge "
A
ppend all ICC
P
erforma
n
ce
f
lags
only to Release
.
.
.
commit
|
commitdiff
|
tree
2012-02-02
Teemu
Murtola
Me
r
g
e
"Revert "F
i
x ICC o
n
W
i
ndows Build"
"
into rele
a
se
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
David van der Spoel
Merge
"F
i
xed error message to identify
the co
r
r
ect
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
David
v
an d
e
r Spoel
Merge
"
Fixed tr
j
conv -sub
"
in
t
o
release
-
4-5-p
a
tc
h
es
commit
|
commitdiff
|
tree
2012-02-01
David van der Spo
e
l
Merge "Impro
v
ed er
r
or messag
e
" into re
l
ease-4-
5
-patches
commit
|
commitdiff
|
tree
2012-02-01
Christoph Junghans
Me
r
g
e "Fi
x
si
g
ned/unsigned w
a
rn
i
ngs"
i
n
t
o re
l
ease-4
.
.
.
commit
|
commitdiff
|
tree
2012-01-31
Roland
S
c
h
u
l
z
R
eve
r
t "Fix ICC on Window
s
Bui
l
d"
commit
|
commitdiff
|
tree
2012-01-31
David va
n
der Spoel
Merge "Fi
x
ICC
o
n
Windows B
u
il
d
" into re
l
e
ase-4-5-patche
s
commit
|
commitdiff
|
tree
2012-01-31
Mark
A
braham
Merge "C
o
rrect
e
d
u
se of ?: in co
n
ditional"
into re
l
ease
.
.
.
commit
|
commitdiff
|
tree
2012-01-25
Roland Schulz
M
e
r
g
e
"New a
p
proach for GerritBuil
d
script" into release
.
.
.
commit
|
commitdiff
|
tree
2012-01-20
David van der Spoel
Merge "Fixed timing measu
r
e
m
ents
.
" int
o
relea
s
e-4-5
.
.
.
commit
|
commitdiff
|
tree
2012-01-15
Christ
o
ph Junghans
Merge "Added CMake Toolchain file for
Blue
G
ene/P" into
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
Christoph Junghans
Merge "Documented the functi
o
n
o
f g_cluster -cl -noav
.
.
.
commit
|
commitdiff
|
tree
2011-12-27
Ro
l
and
S
chulz
Merge
"Added -dhdl to
t
pr fi
l
e l
i
st, fixes #855"
into
.
.
.
commit
|
commitdiff
|
tree
2011-12-20
Ro
l
and S
c
hulz
Me
r
ge
"Usi
n
g
MinSizeRel configur
a
tion an
d
Release target
.
.
.
commit
|
commitdiff
|
tree
2011-12-20
Roland Schulz
Me
r
ge c
h
ange
s
Ia
f
4
c
56b
7
,Ibabed87f
into release-4-5
.
.
.
commit
|
commitdiff
|
tree
2011-12-14
Roland Schulz
Merge "Re-fixed static linkin
g
of maths libraries under
.
.
.
commit
|
commitdiff
|
tree
2011-12-13
Roland Sch
u
l
z
Merge "Relaxed some ass
u
m
ptions
a
bout trajectory times
.
.
.
commit
|
commitdiff
|
tree
2011-12-11
Roland Schulz
Merg
e
"Set -DMPI only if
compiled for FA
H
" into
r
eleas
e
.
.
.
commit
|
commitdiff
|
tree
2011-12-08
Ro
l
and Schulz
Merge "Fix selection parsing in do
u
bl
e
precision
.
"
.
.
.
commit
|
commitdiff
|
tree
2011-12-08
Roland Schulz
Merge "Avoid possible
warnin
g
s i
f
H
U
GE_VAL != infinity
.
.
.
commit
|
commitdiff
|
tree
2011-11-27
Rolan
d
S
chulz
Mer
g
e "Initial
i
ze variables to make GCC 4
.
6 not
complain
.
.
.
commit
|
commitdiff
|
tree
2011-11-24
Roland Schulz
Merge "Fixed g_angle -f -or
t
o copy
t
i
m
es from -f
t
o
.
.
.
commit
|
commitdiff
|
tree
2011-11-08
C
h
ristoph J
u
n
g
hans
Merge "Fixed bu
g
#830
(
s
egv in do_dssp)" into re
l
ease
.
.
.
commit
|
commitdiff
|
tree
2011-11-08
Kasso
n
M
erge "Fix for GB,
d
ouble, SSE2 a
n
d
opt
i
mized kernels
.
.
.
commit
|
commitdiff
|
tree
2011-10-20
C
hristoph J
u
ngha
n
s
M
erge "Fixes for
G
B kernel" into
release-4
-
5
-patches
commit
|
commitdiff
|
tree
2011-10-19
Teemu Murtola
Merge "fixed pull constraining doing n
o
thing,
f
ixes
.
.
.
commit
|
commitdiff
|
tree
2011-09-27
Ross
e
n Aposto
l
o
v
Mer
g
e "Removed CMak
e
wa
r
n
i
ng for recent OpenMPI
v
e
rsions
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
Rossen Apostolov
Merge "Resolved
gerri
t
i
s
su
e
https://gerrit
.
grom
a
cs
.
.
.
commit
|
commitdiff
|
tree
2011-09-16
Rosse
n
Apostolov
Merge
"g_wham
:
fixed pullx
.
xvg reading is
s
ue
w
ith
pull_geom
e
.
.
.
commit
|
commitdiff
|
tree
2011-09-16
Erik Lindahl
Merge
"made
a
llocation for LINCS with parti
c
le decomposition
.
.
.
commit
|
commitdiff
|
tree
2011-09-15
Be
r
k He
s
s
Merge "Intr
o
duced diffe
r
ent options for
pdb2gmx termin
i
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Rossen Apostolov
Merge "Adde
d
warning
line
.
" into
r
elease-4-5-patche
s
commit
|
commitdiff
|
tree
2011-09-13
Berk Hess
Merge
"
F
i
x pdb2
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debug and
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hd
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fil
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s" into releas
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2011-09-13
Berk He
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Merge "Fixed charge groups of CHARMM27 DNA/RNA
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2011-09-13
B
erk
Hess
Me
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ge "Add
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d ACE and CT3
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CHARMM27 a
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