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Work around expanded ensemble issues
2018-10-31
Berk Hess
W
ork
a
round expanded ensembl
e
issues
commit
|
commitdiff
|
tree
2018-10-26
B
erk Hess
Add mi
s
sing mass t
e
r
m
to
d
eltaH
commit
|
commitdiff
|
tree
2018-10-11
Pa
u
l Bauer
Add short securi
t
y
n
otice
commit
|
commitdiff
|
tree
2018-09-04
Mark Abraham
C
larify initial
D
D cell choice with
pr
e
ssure coupli
n
g
commit
|
commitdiff
|
tree
2018-08-24
Mar
k
Ab
r
aha
m
F
ix build without TNG
commit
|
commitdiff
|
tree
2018-08-22
Paul
B
a
u
er
Fix
trjc
o
nv when running wit
h
o
u
t a structure fil
e
commit
|
commitdiff
|
tree
2018-08-20
Be
r
k Hess
Refacto
r
calc_
v
e
r
let_buffer_size()
commit
|
commitdiff
|
tree
2018-08-20
Szilá
r
d Páll
D
isable si
n
g
l
e
compilation
u
nit wit
h
CUD
A
9
.
0
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix Verlet b
u
f
f
e
r
e
stimate with B
D
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix assertion failure
i
n
CG
commit
|
commitdiff
|
tree
2018-08-20
Ber
k
Hess
R
e
ally fix CG wi
t
h
m
ul
t
iple domain
s
commit
|
commitdiff
|
tree
2018-08-14
Mark Abraham
Fix enforced rotat
i
on energy out
p
ut
commit
|
commitdiff
|
tree
2018-07-30
Mark
A
braham
F
i
x CG wit
h
m
ultip
l
e
domains
commit
|
commitdiff
|
tree
2018-07-30
Paul Bauer
Fix b
f
ac
t
or output
commit
|
commitdiff
|
tree
2018-07-29
S
z
ilárd Pál
l
Co
r
rec
t
i
ons
to t
h
e user guide mdrun
p
erf s
e
ction
commit
|
commitdiff
|
tree
2018-07-18
M
a
rk
A
b
r
aha
m
F
i
x
p
r
e-submit matrix
commit
|
commitdiff
|
tree
2018-06-14
Ma
r
k
Ab
r
a
h
am
Updated to prepare for 20
1
8
.
3 release
commit
|
commitdiff
|
tree
2018-06-14
Mark Abraham
Version
2
0
18
.
2
commit
|
commitdiff
|
tree
2018-06-13
Mark A
b
rah
a
m
Fix
p
rem
a
ture
r
e
p
orting o
f
action when GPUs are not
.
.
.
commit
|
commitdiff
|
tree
2018-06-13
M
ark
A
b
r
aham
Updat
e
to
p
-level RE
A
D
ME
commit
|
commitdiff
|
tree
2018-06-13
Mark Abraham
Fixed documentation
t
y
po
commit
|
commitdiff
|
tree
2018-06-12
Berk Hess
A
dd AWH conti
n
uation consistency ch
e
cking
commit
|
commitdiff
|
tree
2018-06-12
Mark Abra
h
am
More fixes to
s
uit
gcc
8
for double buil
d
commit
|
commitdiff
|
tree
2018-06-12
Szilár
d
Páll
Also
i
ssue OM
P
_
N
UM
_
THREADS rea
d
in
g
note to th
e
lo
g
commit
|
commitdiff
|
tree
2018-06-12
Viveca Lindah
l
C
h
anged histo
g
r
a
m ch
e
c
k interval for
m
ultidi
m
ens
i
onal
.
.
.
commit
|
commitdiff
|
tree
2018-06-12
B
e
r
k
Hess
Add fatal error
for i
n
consiste
n
t
gr
a
p
h
commit
|
commitdiff
|
tree
2018-06-12
Berk Hess
Avoid COM remo
v
al moving fr
o
zen atoms
commit
|
commitdiff
|
tree
2018-06-12
Berk
H
e
s
s
Remove
constraint v cor
r
ection for
f
rozen atoms
commit
|
commitdiff
|
tree
2018-06-06
B
e
rk Hess
Fix MPI inconsistency in EM after cons
t
raint failure
commit
|
commitdiff
|
tree
2018-05-22
A
leksei Iupinov
R
e
mo
v
e
unus
e
d r
e
su
l
ts of cudaStreamQuery()
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupinov
Prevent OpenCL timing memory leak
commit
|
commitdiff
|
tree
2018-04-03
M
a
rk Abraham
Re
m
ove leftove
r
m
ention
of twin-
r
ange scheme
commit
|
commitdiff
|
tree
2018-03-27
M
a
rk Abraham
Clarified
mdp
op
t
ion
s
rela
t
ing t
o
bonds
commit
|
commitdiff
|
tree
2018-03-27
M
ark Abraham
More gcc-8 fixes for POWER
commit
|
commitdiff
|
tree
2018-03-21
Mark Abr
a
ham
Versi
o
n 2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mar
k
Abraham
Merge "Merge branch re
l
ease-2016 into release-201
8
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mar
k
Abraha
m
Up
d
ate release notes for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
M
e
r
g
e bran
c
h rele
a
se
-
2
0
16 into
release-2018
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Upda
t
e
u
se of gp
u
_
id in
J
enkins
commit
|
commitdiff
|
tree
2018-03-20
Be
r
k
Hess
Disallow s
i
ngle simulation with multisim
commit
|
commitdiff
|
tree
2018-03-20
Mar
k
Abraha
m
Up
d
ate use of gpu
_
id
i
n
Jenk
i
ns
commit
|
commitdiff
|
tree
2018-03-19
Mark Abrah
a
m
Fix VSX
SIMD wit
h
gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Ber
k
Hess
Cor
r
e
c
t P
M
F sign error in AWH bias s
h
a
ring
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Improve i
n
t
er-simulation signalin
g
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix mdrun signalling with AW
H
bia
s
sharing
commit
|
commitdiff
|
tree
2018-03-13
Berk H
e
ss
Add AWH fixes to release notes
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AW
H
ensem
b
le
c
hec
k
pointing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH deconvolut
i
on when sharin
g
a b
i
a
s
commit
|
commitdiff
|
tree
2018-03-13
S
z
ilá
r
d Páll
Fix cla
n
g 6
.
0
with CUDA 9
.
0
commit
|
commitdiff
|
tree
2018-03-09
Ber
k
Hess
Corr
e
ct pdb2gmx -miss
i
ng option
commit
|
commitdiff
|
tree
2018-03-06
Mark
Abraham
F
ixed
dvdlambda for SHAKE + FE
commit
|
commitdiff
|
tree
2018-03-05
Szilárd Pá
l
l
Add t
o
the contr
i
butor secti
o
n
commit
|
commitdiff
|
tree
2018-03-01
Berk H
e
ss
Detect A
M
D
SMT
topology
commit
|
commitdiff
|
tree
2018-02-27
Mar
k
A
braham
Fix GPU utils test
commit
|
commitdiff
|
tree
2018-02-26
Mark
Abraham
Permit defin
e
.
mdp field to ass
i
gn
value
s
commit
|
commitdiff
|
tree
2018-02-26
M
ark Abr
a
ham
Organize for record
i
ng
2
016-era release n
o
tes and add
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
Be
r
k Hess
Fix md i
n
tegr
a
tor with Nose-Hoover c
o
upling
commit
|
commitdiff
|
tree
2018-02-16
Mark A
b
raham
Merge branch release-2016 int
o
release-2018
commit
|
commitdiff
|
tree
2018-02-16
M
ar
k
Abraham
Bumped pa
t
ch versio
n
for
n
ext releas
e
commit
|
commitdiff
|
tree
2018-02-16
Ber
k
Hess
Correct multisim MPI barrier
commit
|
commitdiff
|
tree
2018-02-16
M
ark Abraham
Version 2016
.
5
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraha
m
M
er
g
e branch
re
l
ease-
2
016 into
r
elease-20
1
8
commit
|
commitdiff
|
tree
2018-02-14
Berk Hes
s
Fix range bu
g
in add_selection_gro
u
ps in t
n
gio
.
c
p
p
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp net char
g
e che
c
k
commit
|
commitdiff
|
tree
2018-02-14
Berk H
e
ss
Fix grompp net charg
e
c
h
e
ck
commit
|
commitdiff
|
tree
2018-02-14
Mar
k
A
braham
Prepare relea
s
e n
o
tes for 2018
.
1
commit
|
commitdiff
|
tree
2018-02-13
Mark
Abrah
a
m
U
s
e death test only when
s
up
p
orte
d
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraha
m
Merge
"M
e
rge branch release-2016 into release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Mark
A
b
raham
Merge
b
r
anc
h
re
l
ease-2
0
16
into release-2018
commit
|
commitdiff
|
tree
2018-02-06
Mark A
b
r
a
h
am
Prev
e
nt log
f
ile energy aver
a
ge
p
rint
i
ng di
v
id
i
ng
by
.
.
.
commit
|
commitdiff
|
tree
2018-01-24
Mark Abraham
Move Win
d
o
w
s i
c
c co
n
fig to post-submit testing
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Fix COMM rem
o
val on part of the syst
e
m
commit
|
commitdiff
|
tree
2018-01-17
Alek
s
ei Iupi
n
ov
Fix box
s
caling in PME mi
x
e
d mo
d
e
commit
|
commitdiff
|
tree
2018-01-17
B
erk
H
ess
R
e-
e
nable GP
U
with wa
l
ls and 1
energy group
commit
|
commitdiff
|
tree
2018-01-16
Be
r
k Hess
Av
o
id mdru
n
e
c
h
o
ing "No option -multi"
commit
|
commitdiff
|
tree
2018-01-11
Mark Abraham
Bump
e
d versi
o
n
f
or ne
x
t
p
atch release
commit
|
commitdiff
|
tree
2018-01-11
Mar
k
Abraham
V
e
rsion 2018
commit
|
commitdiff
|
tree
2018-01-11
M
ark Abraham
Announce in
user log
f
iles
t
hat features are de
p
recated
.
commit
|
commitdiff
|
tree
2018-01-11
Roland Schul
z
Fix GM
X
_ENABLE_AVX512
_
TESTS being in
t
ernal
commit
|
commitdiff
|
tree
2018-01-10
M
ark
Abraham
Fix
auto
m
a
ted GPU I
D
assignment
commit
|
commitdiff
|
tree
2018-01-10
S
z
ilárd Páll
User guide upda
t
es t
o
GPU section
commit
|
commitdiff
|
tree
2018-01-10
Szilárd Páll
Release no
t
es t
w
eaks
commit
|
commitdiff
|
tree
2018-01-10
Mark
A
bra
h
a
m
Ad
d
release no
t
e
s
to s
o
urce r
e
p
o
commit
|
commitdiff
|
tree
2018-01-10
Erik Li
n
d
a
hl
Im
p
rove pdb
2
g
m
x for nonstanda
r
d
residue t
y
pes
commit
|
commitdiff
|
tree
2018-01-10
Szilárd
P
áll
Install gu
i
d
e up
d
at
e
s
commit
|
commitdiff
|
tree
2018-01-10
Szilárd Páll
E
nviro
n
ment v
a
r
iable
d
oc
s
maintenanc
e
commit
|
commitdiff
|
tree
2018-01-10
Alek
s
ei Iup
i
nov
Do not
p
rint PME counter b
r
e
a
kdown if
i
t's em
p
t
y
commit
|
commitdiff
|
tree
2018-01-10
M
ark Abraham
Han
d
le err
o
neous comma
n
d line args bette
r
commit
|
commitdiff
|
tree
2018-01-10
Erik L
i
ndahl
C
lari
f
ie
d
gmx rmsf documen
t
ation
commit
|
commitdiff
|
tree
2018-01-09
Mark Abraham
Clean up
u
s
er guide f
o
r
release
commit
|
commitdiff
|
tree
2018-01-09
Mark Abra
h
am
Me
r
ge branch release-2016 into release-2018
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Do not tu
r
n on DLB at
r
eplica exchange
commit
|
commitdiff
|
tree
2018-01-04
E
rik
L
indahl
Implement changes fo
r
CMake policy 0
0
68
commit
|
commitdiff
|
tree
2018-01-04
M
ark Abrah
a
m
Add t
e
st
c
onfig of GPU bu
i
ld on sl
a
ve
without GPU
commit
|
commitdiff
|
tree
2018-01-04
Paul Ba
u
er
Fix gmx msd when usi
n
g
C
OM
re
m
oval and molecules
commit
|
commitdiff
|
tree
2018-01-03
Erik
L
indahl
Fix ind
e
x err
o
r in gmx chi
commit
|
commitdiff
|
tree
2018-01-03
Paul
Bauer
C
o
rrect dihedral
restraint section in Manual
commit
|
commitdiff
|
tree
2018-01-03
Erik Lindahl
Avoid FTZ trigger
i
ng simd test fa
i
l
u
r
e
s
commit
|
commitdiff
|
tree
2018-01-02
Erik Lindahl
F
i
x
O
penCL
c
o
m
piles on Mac
OS
commit
|
commitdiff
|
tree
2018-01-02
Erik Lin
d
a
h
l
Impr
o
ve
m
anual from comments by
Gang
Liu
commit
|
commitdiff
|
tree
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