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Merge "Merge branch release-2016 into release-2018" into release-2018
2018-03-21
Ma
r
k Abraham
Merge "Merge branch release-2016
i
n
to release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Updat
e
release notes for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Ma
r
k Abraham
Merge b
r
anc
h
releas
e
-201
6
int
o
r
elease-2018
commit
|
commitdiff
|
tree
2018-03-20
M
ark Abraham
Update u
s
e of gpu_id
in
Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disallow single simul
a
t
ion w
i
th multisim
commit
|
commitdiff
|
tree
2018-03-20
M
a
rk Abraham
U
pdate use of gpu
_
id in Jenki
n
s
commit
|
commitdiff
|
tree
2018-03-19
Mark Abraham
F
ix V
S
X
S
IMD wit
h
gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Correct P
M
F sign er
r
or in AWH
b
i
as sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk
Hess
Improve inter-simulation signaling
commit
|
commitdiff
|
tree
2018-03-14
B
e
rk Hess
Fix
mdrun signal
l
i
ng with
A
W
H bias sharing
commit
|
commitdiff
|
tree
2018-03-13
Berk H
e
ss
Add
AWH
fixes to
release not
e
s
commit
|
commitdiff
|
tree
2018-03-13
Be
r
k Hess
Fix
AWH ensem
b
le
checkpointing
commit
|
commitdiff
|
tree
2018-03-13
Berk
H
e
ss
Fix
AWH d
e
co
n
volu
t
i
o
n
w
hen sharing a
bias
commit
|
commitdiff
|
tree
2018-03-13
Szilárd Páll
Fix clang 6
.
0 with C
U
DA 9
.
0
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
Corr
e
c
t
pdb2gmx
-m
i
ssing option
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
Fixed dvdlambda f
o
r SHAKE +
F
E
commit
|
commitdiff
|
tree
2018-03-05
Szi
l
árd Páll
Ad
d
to the contri
b
utor sect
i
on
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Det
e
ct A
M
D SMT topology
commit
|
commitdiff
|
tree
2018-02-27
Mark Abraham
Fix GPU ut
i
ls test
commit
|
commitdiff
|
tree
2018-02-26
Ma
r
k Abraham
Permit d
e
fine
.
mdp fi
e
ld to assi
g
n values
commit
|
commitdiff
|
tree
2018-02-26
M
ark
Abraham
Organize for recording
20
1
6-era release
not
e
s and add
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
Berk
H
ess
Fix m
d
integrator wi
t
h Nose-H
o
over
coupli
n
g
commit
|
commitdiff
|
tree
2018-02-16
Ma
r
k
Abraham
M
e
rge
b
ranch rel
e
ase-2016 into release-2018
commit
|
commitdiff
|
tree
2018-02-16
M
a
rk
A
braham
Bu
m
ped
p
atch ver
s
io
n
for next releas
e
commit
|
commitdiff
|
tree
2018-02-16
B
e
rk Hess
C
orrect
m
ultisim MPI
b
arri
e
r
commit
|
commitdiff
|
tree
2018-02-16
Mark Ab
r
aham
Ve
r
s
ion 2016
.
5
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
Merge branc
h
release-2016 into release-201
8
commit
|
commitdiff
|
tree
2018-02-14
B
e
rk He
s
s
Fix
range bug in add
_
sele
c
tion
_
g
r
oups in
tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Ber
k
Hess
Fix grompp net charge check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fi
x
grompp net charge check
commit
|
commitdiff
|
tree
2018-02-14
M
ark Abraham
Pr
e
pare
r
elease notes for
2018
.
1
commit
|
commitdiff
|
tree
2018-02-13
Mark Abraham
Use dea
t
h test
only when s
u
pported
commit
|
commitdiff
|
tree
2018-02-08
Ma
r
k A
b
r
a
h
a
m
Merg
e
"Merge branch rele
a
se-2
0
16 in
t
o release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
M
a
rk Abraham
Merge branch
release-
2
01
6
i
nto
release-201
8
commit
|
commitdiff
|
tree
2018-02-06
Mark Abraham
Pr
e
vent
log file energy average printing dividin
g
by
.
.
.
commit
|
commitdiff
|
tree
2018-01-24
Mark Abrah
a
m
M
ove Wi
n
dows icc
c
onf
i
g to p
o
st-submit tes
t
ing
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Fix COMM
removal on part
o
f
the system
commit
|
commitdiff
|
tree
2018-01-17
Al
e
ksei I
u
pinov
Fix box scali
n
g
i
n PME mixed mod
e
commit
|
commitdiff
|
tree
2018-01-17
B
e
r
k Hess
Re-ena
b
le GPU with
w
alls and 1
energy group
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
A
void md
r
un echoing "No option
-
multi"
commit
|
commitdiff
|
tree
2018-01-11
M
a
rk Abraham
Bumped ve
r
sion for
n
ext patch release
commit
|
commitdiff
|
tree
2018-01-11
M
a
r
k
Abraham
Ver
s
ion 20
1
8
commit
|
commitdiff
|
tree
2018-01-11
Mark
A
b
r
a
h
am
Announce in user log files that f
e
atures ar
e
d
eprecated
.
commit
|
commitdiff
|
tree
2018-01-11
Roland Schulz
Fix GMX_ENABLE_AVX5
1
2_TEST
S
being
i
nternal
commit
|
commitdiff
|
tree
2018-01-10
Mark Ab
r
aham
Fix autom
a
t
e
d
GPU ID assign
m
ent
commit
|
commitdiff
|
tree
2018-01-10
S
z
i
lárd P
á
ll
User guide updates to GPU section
commit
|
commitdiff
|
tree
2018-01-10
Sz
i
lárd Páll
Release n
o
tes tweaks
commit
|
commitdiff
|
tree
2018-01-10
Mark Abraham
Add rele
a
s
e
not
e
s to sour
c
e repo
commit
|
commitdiff
|
tree
2018-01-10
Erik Lin
d
ahl
Im
p
rove pdb2gmx
f
or
n
o
nstandard residue types
commit
|
commitdiff
|
tree
2018-01-10
Sz
i
lá
r
d
P
áll
I
nstall guide up
d
ates
commit
|
commitdiff
|
tree
2018-01-10
Szilárd P
á
l
l
E
nvironm
e
nt variable docs
m
aintenanc
e
commit
|
commitdiff
|
tree
2018-01-10
Aleksei
I
upinov
Do not print PME
counte
r
break
d
own if
i
t
's empty
commit
|
commitdiff
|
tree
2018-01-10
M
a
rk Abraham
Ha
n
dle
e
rroneous c
o
m
m
and line args better
commit
|
commitdiff
|
tree
2018-01-10
Erik
L
indahl
Clarified
g
m
x rm
s
f
docu
m
entatio
n
commit
|
commitdiff
|
tree
2018-01-09
M
a
rk Abr
a
ham
C
lean up use
r
gu
i
de for
r
elease
commit
|
commitdiff
|
tree
2018-01-09
Mar
k
A
b
rah
a
m
Merge br
a
nch r
e
le
a
s
e-2016 into re
l
ease-2018
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Do
n
ot turn on DL
B
a
t
replica
e
xchange
commit
|
commitdiff
|
tree
2018-01-04
Erik Linda
h
l
I
mplem
e
nt chang
e
s fo
r
C
M
ake p
o
licy 0068
commit
|
commitdiff
|
tree
2018-01-04
Mark Abraham
Add
test confi
g
of GPU build on slave wi
t
hout GP
U
commit
|
commitdiff
|
tree
2018-01-04
P
aul Bau
e
r
F
ix gmx
m
s
d when using COM
r
emoval and molecules
commit
|
commitdiff
|
tree
2018-01-03
Erik Lindah
l
Fix index error in gmx chi
commit
|
commitdiff
|
tree
2018-01-03
Paul Bau
e
r
Corr
e
ct dihedral restr
a
int sect
i
o
n
in Manua
l
commit
|
commitdiff
|
tree
2018-01-03
E
rik Lindahl
A
void FTZ triggerin
g
s
i
m
d te
s
t failure
s
commit
|
commitdiff
|
tree
2018-01-02
E
r
i
k
Lindahl
F
i
x
O
penCL compile
s
on Ma
c
OS
commit
|
commitdiff
|
tree
2018-01-02
Erik Lind
a
h
l
Improve manual
f
rom
c
omme
n
ts by Ga
n
g Liu
commit
|
commitdiff
|
tree
2018-01-02
Erik Lindahl
M
a
ke it e
x
plicit th
a
t time
uni
t
s apply to begin/en
d
.
.
.
commit
|
commitdiff
|
tree
2018-01-02
E
r
ik Lindahl
Don't require matching nam
e
s between
rtp
an
d
tdb files
commit
|
commitdiff
|
tree
2018-01-02
E
r
ik Lindahl
Don't writ
e
refere
n
ce pu
l
l group 0 to log
commit
|
commitdiff
|
tree
2017-12-30
Mark Abraham
First rele
a
se c
a
ndidate
f
or version 2018
commit
|
commitdiff
|
tree
2017-12-26
Erik L
i
ndahl
Fix
bui
l
ds on AR
M
& clarif
y
(A
R
M) GPU support
commit
|
commitdiff
|
tree
2017-12-22
M
a
rk A
b
raham
Merge br
a
nch release-2016 into
r
elease-201
8
commit
|
commitdiff
|
tree
2017-12-21
M
a
rk Abraha
m
Merge bran
c
h releas
e
-
5
-1
i
nto
release-
2
016
commit
|
commitdiff
|
tree
2017-12-21
Mark Ab
r
aham
Bump min
o
r version for theoretical new release
commit
|
commitdiff
|
tree
2017-12-21
P
a
sc
a
l Merz
Do
c
umentation and fixes for physical validation
commit
|
commitdiff
|
tree
2017-12-21
Mark Abra
h
a
m
Up
d
ate doubl
e
-prec
i
sion te
s
t configurati
o
ns
commit
|
commitdiff
|
tree
2017-12-21
Ro
l
and Schulz
Update c
h
ecks for BuildOwnFFT
commit
|
commitdiff
|
tree
2017-12-20
Mark
Abraham
Use ne
w
defaultReal
T
ol
e
r
ance()
to
stabilise
some te
s
ts
commit
|
commitdiff
|
tree
2017-12-20
Mark Abraham
Merge "
M
erge branch release-2016 into release-201
8
.
.
.
commit
|
commitdiff
|
tree
2017-12-20
Mark Abraham
M
erge branch release-2016 into release-2018
commit
|
commitdiff
|
tree
2017-12-19
M
a
r
k Abraham
Third be
t
a release
of
2
018
commit
|
commitdiff
|
tree
2017-12-19
M
a
rk Abraham
Fix table te
s
ts and improve t
a
ble
c
onstr
u
c
t
ion
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make oversubscription warnin
g
cons
i
stent
commit
|
commitdiff
|
tree
2017-12-19
Carsten Kutzner
Fix electric field
.
mdp document
a
t
ion
commit
|
commitdiff
|
tree
2017-12-19
Erik Lin
d
ahl
U
se reduced de
f
ault
tolerances for tpx c
o
m
pariso
n
commit
|
commitdiff
|
tree
2017-12-18
Roland Schulz
Fix cmake e
r
ror
w
i
t
h emacs lock files in p
l
ace
commit
|
commitdiff
|
tree
2017-12-17
R
ol
a
nd
Schulz
Change
a
vx_128
_
fma
b
u
ild t
o
dou
b
le
commit
|
commitdiff
|
tree
2017-12-17
Rola
n
d Schulz
Su
p
port Simd4N for
S
imd
R
ealWidth<
4
commit
|
commitdiff
|
tree
2017-12-14
Erik Lind
a
hl
Fix PBC error in g
m
x_spatia
l
commit
|
commitdiff
|
tree
2017-12-14
Mark Abraham
Merg
e
"Merge branch release-201
6
into
release-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-12
Erik Lindahl
Disallow ascii
f
o
rmats for gm
x
t
r
j
cat
commit
|
commitdiff
|
tree
2017-12-12
M
a
rk Abraham
Im
p
r
ove gro
m
pp missing-parameter
s
error m
e
ssage
commit
|
commitdiff
|
tree
2017-12-12
Mark Abr
a
h
am
Mer
g
e
b
ranch release-2016 i
n
to releas
e
-20
1
8
commit
|
commitdiff
|
tree
2017-12-11
Mark Abraham
Second beta releas
e
of 2018
commit
|
commitdiff
|
tree
2017-12-11
E
r
ik Lindahl
Remove duplicated lines from OPLS ffb
o
nded
.
itp
commit
|
commitdiff
|
tree
2017-12-11
Ro
l
and Schulz
Replace int
r
ins
i
c with
i
nlin
e
asm fo
r
A
VX512 unit
t
e
s
t
commit
|
commitdiff
|
tree
2017-12-11
Eri
k
L
i
ndah
l
D
o
n'
t
war
n
a
bout
N
VML
clocks that ar
e
at max
commit
|
commitdiff
|
tree
2017-12-11
Ber
k
Hess
Add grompp note for PR pcoup
l
e + posi
t
ion restraints
commit
|
commitdiff
|
tree
2017-12-10
Erik Lindahl
Revert "Disable default-on NVML support
i
n CMake"
commit
|
commitdiff
|
tree
2017-12-07
E
rik Lindahl
Added co
o
l quote
from Vi
v
eca's defe
n
se
commit
|
commitdiff
|
tree
2017-12-07
Roland S
c
hulz
Fix
A
W
H t
e
s
t accuracy
commit
|
commitdiff
|
tree
next