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Added references to ProtSqueeze and g_membed to the user guide
2016-04-03
Semen Yesylev
s
kyy
Added references to P
r
otSque
e
ze and
g
_me
m
b
e
d to the
.
.
.
commit
|
commitdiff
|
tree
2016-04-02
R
oland S
c
hulz
Fix
c
o
ol
q
u
o
tes
commit
|
commitdiff
|
tree
2016-04-01
M
a
rk Abraham
Revert to treating -1
as "ge
n
era
t
e a
seed" in
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
B
erk He
s
s
Add option for
external pull poten
t
ial
commit
|
commitdiff
|
tree
2016-03-31
Sz
i
lárd Páll
refactor CUDA tex
t
u
r
e-bas
e
d t
a
ble
initiali
z
ation
commit
|
commitdiff
|
tree
2016-03-31
Szil
a
rd Pall
avoid CPU oversubscription with GP
U
s
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Páll
L
J
combination
r
u
l
e kern
e
ls
f
or OpenCL
commit
|
commitdiff
|
tree
2016-03-30
Sz
i
lárd Páll
R
e-enable i-ato
m
type
loca
l
mem
p
r
efetch in OpenCL
commit
|
commitdiff
|
tree
2016-03-30
T
eemu Murt
o
la
Make includesorter
.
py
w
or
k
with
D
oxygen 1
.
8
.
10+
commit
|
commitdiff
|
tree
2016-03-30
S
z
i
lár
d
P
á
l
l
Describe AMD APPSDK 3
.
0 is
s
ues in the g
u
ide
commit
|
commitdiff
|
tree
2016-03-30
Tee
m
u Mu
r
tola
Fix error reporting fo
r
documentation b
u
ild
commit
|
commitdiff
|
tree
2016-03-30
Mark Abraha
m
Clean up vs
i
t
e
code
commit
|
commitdiff
|
tree
2016-03-22
Carsten Kutzn
e
r
Clea
n
-
u
p code f
o
r swapcoords
.
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
LJ combination ru
l
e kerne
l
s for CUDA
commit
|
commitdiff
|
tree
2016-03-19
Ma
r
k
A
braham
A
dd
m
ore const correctnes
s
commit
|
commitdiff
|
tree
2016-03-19
M
ark Abraham
Improved some m
d
ru
n
i
n
te
g
rati
o
n tests
commit
|
commitdiff
|
tree
2016-03-18
Viveca Lindahl
Added pu
l
l coordinate ge
o
me
t
r
y
angle
.
commit
|
commitdiff
|
tree
2016-03-18
Davi
d
van der Spo
e
l
F
ix
e
d division by z
e
ro in
po
l
arize
.
commit
|
commitdiff
|
tree
2016-03-18
Nicholas Bre
e
n
Va
r
ious m
i
nor spe
l
ling fixe
s
- messages and code
c
o
mmen
t
s
.
.
.
commit
|
commitdiff
|
tree
2016-03-17
C
arste
n
Kutzner
Fix m
e
mbed initialization
commit
|
commitdiff
|
tree
2016-03-10
Mark A
b
rah
a
m
Require 2015 version for M
S
VC
commit
|
commitdiff
|
tree
2016-02-27
Berk
H
ess
Remove epsfac from GPU k
e
rnel inne
r
-lo
o
ps
commit
|
commitdiff
|
tree
2016-02-23
Mark Abraham
Replace cppcheck suppression in checkpo
i
n
t
c
ode
commit
|
commitdiff
|
tree
2016-02-16
Mark Abraham
Merge branc
h
relea
s
e-5-
0
into relea
s
e
-
5-1
commit
|
commitdiff
|
tree
2016-02-14
M
ar
k
Ab
r
aham
R
e-generat
e
d eps for figure 4
.
8
commit
|
commitdiff
|
tree
2016-02-10
Mark
A
braham
Re-remo
v
e *_stochd_state fun
c
tion de
c
l
aration
s
commit
|
commitdiff
|
tree
2016-02-10
Erik Lindahl
Scalar functions m
i
mick
i
ng the
S
IMD inte
r
face
commit
|
commitdiff
|
tree
2016-02-08
Mark Abr
a
ham
Me
r
ge branch relea
s
e-5-0 into release-5-1
commit
|
commitdiff
|
tree
2016-02-06
Mark Abraham
Merge branch release-5-
1
commit
|
commitdiff
|
tree
2016-02-03
Mark
A
braham
Bump
e
d
p
atch num
b
er to prepar
e
fo
r
future 5
.
1
.
3
relea
s
e
commit
|
commitdiff
|
tree
2016-02-03
Mark A
b
r
a
ham
Ver
s
ion 5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
Mark
A
braham
M
e
rge rel
e
ase-5
-
0 into
r
e
lease-5-1
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Merg
e
branch release-5-1
commit
|
commitdiff
|
tree
2016-01-28
Mark Abraham
Avoid FP ex
c
eption
commit
|
commitdiff
|
tree
2016-01-27
Mark Ab
r
aham
Mer
g
e branch
r
e
l
ease-5-1
commit
|
commitdiff
|
tree
2016-01-27
M
a
r
k
A
b
r
a
ha
m
Remove bNotLastFrame
commit
|
commitdiff
|
tree
2016-01-26
Mark Abraham
Fix de
f
ault for GMX_U
S
E_NVM
L
commit
|
commitdiff
|
tree
2016-01-25
Mark Ab
r
aham
M
erge branc
h
release-
5
-1
commit
|
commitdiff
|
tree
2016-01-12
Mark Abraham
Merge branch release-5-0 into
r
e
lease-5-
1
commit
|
commitdiff
|
tree
2016-01-08
Mark A
b
r
a
ham
Merge
b
ranch rel
e
ase-5-1
commit
|
commitdiff
|
tree
2016-01-07
Mark Abra
h
a
m
Fix some mdrun h
e
ade
r
dependenc
i
es
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
A
v
o
id mor
e
C++ bindi
n
gs
f
or MP
I
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Stop using UNDEFIN
E
D
as name of a symbol
commit
|
commitdiff
|
tree
2016-01-07
Mar
k
Abraham
R
emove fie
l
d
s
used only for S
D
2
commit
|
commitdiff
|
tree
2016-01-07
Mark A
b
rah
a
m
Backp
o
rt md-vv fixes
commit
|
commitdiff
|
tree
2016-01-06
Mark Abr
a
ham
Fix spuri
o
us gcc warning
commit
|
commitdiff
|
tree
2015-12-29
Berk
H
e
ss
Correc
t
vector
c
heck of gmx check
commit
|
commitdiff
|
tree
2015-12-29
Teemu M
u
rtola
P
ack
a
ging build sc
r
ipt f
o
r web site
commit
|
commitdiff
|
tree
2015-12-28
M
a
r
k Abrah
a
m
M
erge branch r
e
lease-5-
1
commit
|
commitdiff
|
tree
2015-12-27
M
ark Abraham
Fix some OpenCL issu
e
s
commit
|
commitdiff
|
tree
2015-12-27
B
erk Hess
Reorganized domdec
i
nitializ
a
t
i
on
commit
|
commitdiff
|
tree
2015-12-24
M
ark Abr
a
ham
Shell c
o
de c
l
eanup
commit
|
commitdiff
|
tree
2015-12-24
Erik
Lindahl
IBM Power6 VMX
extended SIMD
commit
|
commitdiff
|
tree
2015-12-17
M
a
rk
Abraham
Simpl
i
f
i
ed e
n
e
r
gy-sum
m
a
t
i
on c
o
de
commit
|
commitdiff
|
tree
2015-12-16
B
e
rk Hess
Add on
e
e
lement
t
o
s
t
at
e
rvec arrays
commit
|
commitdiff
|
tree
2015-12-15
E
r
ik Linda
h
l
C++ math
f
un
c
tio
n
clean
u
p
commit
|
commitdiff
|
tree
2015-12-15
Teem
u
Murtola
M
o
ve main
.
*, split
t
er
.
*,
gmx_omp_nthread
s
.
* to mdlib
commit
|
commitdiff
|
tree
2015-12-15
Teemu Mu
r
tol
a
Move readinp
.
* and warninp
.
* to fileio/
commit
|
commitdiff
|
tree
2015-12-15
Te
e
mu Mur
t
ola
Mov
e
h
ardware dete
c
tion to hardware/
commit
|
commitdiff
|
tree
2015-12-15
Teemu
Murt
o
la
Move so
m
e
mdrun co
d
e
o
ut of gmxlib/
commit
|
commitdiff
|
tree
2015-12-12
Teemu Murtola
Move disre
.
*
and orires
.
*
t
o listed-forc
e
s/
commit
|
commitdiff
|
tree
2015-12-12
Teemu M
u
rt
o
la
Move put_atoms
_
in_box_omp
(
) to si
m
_util
.
*
commit
|
commitdiff
|
tree
2015-12-12
T
eemu Murtola
Remove
topology -
>
file
i
o depen
d
en
c
y
commit
|
commitdiff
|
tree
2015-12-10
Mark Ab
r
aham
Merge branch 'ori
g
in/re
l
ease-5-1'
commit
|
commitdiff
|
tree
2015-12-08
Mark Abraham
Merge branch 'rel
e
ase-
5
-0' into re
l
e
ase-5
-
1
commit
|
commitdiff
|
tree
2015-12-08
M
ark Abraham
Fix Trotter integra
t
ion
commit
|
commitdiff
|
tree
2015-12-03
M
a
r
k
Ab
r
aham
Remo
v
e mdrun -compact
commit
|
commitdiff
|
tree
2015-12-03
Tee
m
u Murto
l
a
Mov
e
str
d
b
.
* to utility/
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
Ma
d
e t_inp
u
t
rec co
n
s
t
i
n PM
E
load balancing
commit
|
commitdiff
|
tree
2015-12-02
Mark Ab
r
aha
m
Remove
t
win-rang
e
scheme
commit
|
commitdiff
|
tree
2015-11-30
Mark Abraham
Refactor ha
r
dwa
r
e
informat
i
on
m
a
n
agement
commit
|
commitdiff
|
tree
2015-11-25
Elton Carval
h
o
Rotate Figu
r
e 8
.
2 in ma
n
ual
.
commit
|
commitdiff
|
tree
2015-11-24
Mark Abraham
Fix
e
r
r
o
r
in multi-sim communication
commit
|
commitdiff
|
tree
2015-11-23
Mark
A
braham
U
pdate
a
nd expand pre-su
b
mit c
o
mmit matr
i
x
commit
|
commitdiff
|
tree
2015-11-16
Mark Abraham
Remov
e
t_a
d
r
e
s
s
commit
|
commitdiff
|
tree
2015-11-16
M
a
r
k
Abraham
Rem
o
ved state_global from mdrun en
e
rgy-
s
ummation
commit
|
commitdiff
|
tree
2015-11-16
Mark Ab
r
a
ham
Merge branch
r
ele
a
se-5-1
commit
|
commitdiff
|
tree
2015-11-15
Mar
k
A
b
raha
m
Remove
AdResS
commit
|
commitdiff
|
tree
2015-11-11
Mark
A
braham
Merg
e
rele
a
se
-
5
-0
into
rel
e
ase-5-
1
commit
|
commitdiff
|
tree
2015-11-10
M
ark Abra
h
am
B
ump
patc
h
version to p
r
epare
f
or 5
.
1
.
2
commit
|
commitdiff
|
tree
2015-11-04
Mark Abraham
Merg
e
branch release-5-
1
commit
|
commitdiff
|
tree
2015-11-04
Mark Abraha
m
Even le
s
s mo
v
in
g
f
rom uniq
u
e_ptr
commit
|
commitdiff
|
tree
2015-11-04
M
ar
k
A
b
raham
V
e
rsion
5
.
1
.
1
commit
|
commitdiff
|
tree
2015-10-28
Mark
A
braham
Sup
p
re
s
s warnings when we
ha
v
e OpenCL 2
.
0 support
commit
|
commitdiff
|
tree
2015-10-15
Sz
i
lárd Páll
Add CUDA nvcc
>
=7
.
0 support
commit
|
commitdiff
|
tree
2015-10-14
Mark A
b
raham
M
erge relea
s
e-5
-
0 into
r
elease-5
-
1
commit
|
commitdiff
|
tree
2015-10-14
Ma
r
k Abraham
Version bumps after release
commit
|
commitdiff
|
tree
2015-10-14
Mark A
b
raham
Simpl
i
fy ge
n
con
f
commit
|
commitdiff
|
tree
2015-10-14
Mark Abraham
V
e
rsion 5
.
0
.
7
commit
|
commitdiff
|
tree
2015-10-13
Mark Abra
h
am
M
e
rge branch releas
e
-4-6
into
relea
s
e-5-0
commit
|
commitdiff
|
tree
2015-10-13
Erik
L
i
n
dahl
Replace GROM
A
CS-specific math funct
i
ons with C+
+
11
.
.
.
commit
|
commitdiff
|
tree
2015-10-07
Mark Ab
r
ah
a
m
Merge branch release-5-1 in
t
o
m
ast
e
r
commit
|
commitdiff
|
tree
2015-10-07
Mark Ab
r
a
h
am
Fixed FFTW detectio
n
s
t
atus messa
g
e location
commit
|
commitdiff
|
tree
2015-10-05
Mark Abraham
M
e
rge release-5-0 in
t
o release-5-
1
commit
|
commitdiff
|
tree
2015-10-02
Mark Abraham
Te
m
po
r
arily t
e
st on a machine with only two GPU
s
commit
|
commitdiff
|
tree
2015-09-28
Mark Abraham
Eliminate
u
se
o
f
typ
e
defs
.
h in
kerne
l
C code
commit
|
commitdiff
|
tree
2015-09-26
Mark Abraham
Fix reacti
o
n-field warnin
g
m
e
ssag
e
commit
|
commitdiff
|
tree
2015-09-22
T
eemu Murtola
Move oenv
.
* to f
i
leio
/
commit
|
commitdiff
|
tree
2015-09-16
Mark Abraham
Remove
G
MX_NOCHARGEGROUPS
commit
|
commitdiff
|
tree
2015-09-16
Szil
a
rd Pall
Fix OpenCL bu
i
l
d
commit
|
commitdiff
|
tree
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