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Small update of the GPU related documentation.
2010-09-01
Rosse
n
Apostolov
Small update of th
e
GPU related d
o
cu
m
entation
.
commit
|
commitdiff
|
tree
2010-09-01
Rossen
A
pos
t
olov
Mer
g
e bra
n
c
h 'release-4-5-patches' of
git
.
gro
m
a
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Ross
e
n A
p
ostolov
Mer
g
e bra
n
ch 'releas
e
-4-5-patc
h
es' of gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Rossen Apostolov
M
e
rge branch
'release
-
4-5-patches
'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Ross
e
n
Apostolov
OpenMM n
o
w a
c
c
e
pts cut
-
off met
h
od, since it's
needed
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
R
o
ssen
A
postolov
New rele
a
se 4
.
5
-
beta4
commit
|
commitdiff
|
tree
2010-08-26
Ros
s
e
n Apostolo
v
Modified the
O
p
enM
M
w
r
apper in
t
erface to support the
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Ro
s
sen Apos
t
olov
Added the g_pm
e
_
error
tool fro
m
Flori
a
n
D
ommert
.
Thanks!
commit
|
commitdiff
|
tree
2010-08-26
Rosse
n
Ap
o
stolov
Fixed h
a
r
dco
d
ed Op
e
nMM
l
i
b
rary name
.
commit
|
commitdiff
|
tree
2010-08-26
R
os
s
en
Apostolov
R
e
moved the u
n
necessary hacks
from some boolean s
t
atements
.
commit
|
commitdiff
|
tree
2010-08-25
Rossen Apostolov
Redefine the d
e
fault bo
o
lea
n
t
y
pe
t
o gmx_
b
o
o
l
.
commit
|
commitdiff
|
tree
2010-08-23
R
o
s
s
en Ap
o
stolov
Merge branch 'release-4-5-pat
c
h
e
s
' of
git
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Rossen A
p
ostolov
F
i
x
e
d a t
y
po a
b
ou
t
non-
e
xis
t
ing macro in OpenMM
commit
|
commitdiff
|
tree
2010-08-19
Ross
e
n Apostolov
Enable the Re
f
e
r
e
n
ce platform for OpenMM
.
commit
|
commitdiff
|
tree
2010-08-18
Ros
s
en Apostolov
Mer
g
e branch '
r
e
l
ease-4-5-
p
a
tches'
o
f g
i
t
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen
Apostolo
v
Fixe
d
t
h
e
e
xecuti
o
n
o
rder in Op
e
nMM
s
o that the generated
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen Apost
o
lov
Preserv
e
the
.
p
l ext
e
ntions to script
s
.
commit
|
commitdiff
|
tree
2010-08-16
Ro
s
sen A
p
ostol
o
v
Removed the nb_kern
e
l
4xx_
i
n
t
el_
s
yn
t
a
x
.
c ent
r
ies from
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Rossen Apos
t
olov
Added support for imp
r
oper
d
ihedral
s
neede
d
fo
r
CHARMM
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Ro
s
sen Apostolo
v
OpenMM:
added s
u
pport for Amb
e
rFF pro
p
er/imprope
r
torsi
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Ros
s
en Apostolov
F
i
xed
a
r
everted ve
r
sion st
r
ing in conf
i
gur
e
.
a
c
commit
|
commitdiff
|
tree
2010-08-12
Rossen
A
postolo
v
Mer
g
e branch 're
l
ea
s
e-4-5-patches' of gi
t
.
grom
a
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen Apostolov
Warni
n
gs about using broken MPI implementations
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen
Apostol
o
v
Updated
the
C
Make scripts for fi
n
ding CU
D
A, LibXml2
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
R
o
sse
n
Apos
t
olo
v
Fixed broken
linking wit
h
single prec
i
si
o
n f
f
tw3 in
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Ro
s
sen
Ap
o
stol
o
v
A
dd
e
d a
new
file INSTALL
.
cmake wit
h
install
a
tion instructio
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Ap
o
stolov
Merge branch
'rel
e
a
s
e-4-
5
-
pat
c
hes
'
o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Ros
s
e
n A
p
os
t
olov
CM
a
k
e builds no
w
install GMXR
C
*
files
.
commit
|
commitdiff
|
tree
2010-08-11
R
ossen
A
pos
t
olov
Fix for
C
Make builds
s
o t
h
at they don't fail
e
v
en when
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Rossen
Ap
o
stolov
Bumpe
d
version to 4
.
5-b
e
ta3
commit
|
commitdiff
|
tree
2010-08-10
Rossen
Ap
o
stolov
F
ixed
a
t
ypo in src/
t
ools
/
CMake
L
i
s
ts
.
txt
.
commit
|
commitdiff
|
tree
2010-08-10
R
osse
n
Aposto
l
ov
Adde
d
mis
s
i
ng
NULL in
c
h
a
inse
p
e
nu
m
in pdb2gmx
.
commit
|
commitdiff
|
tree
2010-08-04
Ros
s
en Apostolov
Fi
x
share/html/onlin
e
/mdp_op
t
.
html
.
commit
|
commitdiff
|
tree
2010-08-04
Rossen Apostolov
F
ixed configur
e
.
ac ty
p
o regrading qmmm-orca
.
commit
|
commitdiff
|
tree
2010-08-02
Rossen A
p
ost
o
lov
New
b
eta rel
e
ase
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen
A
postolov
Added *
.
p
c
.
c
m
akei
n
file
s
f
or distr
i
bution
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
Remo
v
e
d OpenMM inter
f
ace from
autoco
n
f, use
CMake instea
d
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apost
o
lov
Fixed a typo in previous Makefil
e
.
a
m
c
o
mmi
t
commit
|
commitdiff
|
tree
2010-07-29
Rossen
A
p
ostolov
Adde
d
fo
r
d
i
s
tribution s
o
me extra files needed by CMake
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
M
e
rge bran
c
h
'ma
s
ter' of git
.
grom
a
cs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
Fixed
t
y
p
os in p
r
evio
u
s commit
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
Adde
d
missing assembly file
s
in nonbo
n
de
d
/
n
b_kernel_x
8
6_64
_
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Rosse
n
Apostolov
More ma
k
e distchec
k
fixes
.
commit
|
commitdiff
|
tree
2010-07-26
Rossen
A
postolov
make distc
h
eck fixes
commit
|
commitdiff
|
tree
2010-07-23
Ros
s
en Apo
s
t
o
lov
A
d
j
u
st
ewald_rtol wh
e
n pas
s
i
n
g
it to
OpenMM
.
commit
|
commitdiff
|
tree
2010-07-21
Rossen
Apostolov
ewald_rtol adjust
m
ent for OpenMM
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
Ad
d
ed SHAR
E
D_VERSIO
N
_INFO t
o
l
i
bgmxpreprocess
.
commit
|
commitdiff
|
tree
2010-07-20
Ro
s
s
en Apostolov
M
oved
t
he X1
1
automake dependency flag
i
nside ng
m
x
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
Di
s
abl
e
d adjustment of ewald_rtol for OpenMM
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
By d
e
faul
t
GM
X
_AC
C
ELERATION is now
"
auto"
.
commit
|
commitdiff
|
tree
2010-07-20
R
o
s
s
en
Ap
o
stolov
Added s
u
ppor
t
fo
r
OpenM
M
-2
.
0, a
n
d
C
UDA-
3
.
1
is now r
e
q
u
i
red
.
commit
|
commitdiff
|
tree
2010-07-02
R
ossen Apo
s
tolo
v
Disable by defaul
t
ia64 as
s
em
b
ly loops
.
Those will
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Rossen Apos
t
olov
Merge branch 'master' of git
.
gromacs
.
o
rg:
g
romacs
commit
|
commitdiff
|
tree
2010-07-02
Ro
s
s
en Apos
t
olov
Disab
l
e All
v
s
Al
l
ke
r
n
e
ls fo
r
v
e
r
y small systems (<
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Rossen Ap
o
s
tolov
Init
i
al CTest s
u
p
p
ort
commit
|
commitdiff
|
tree
2010-06-23
R
o
ssen
A
postolo
v
Incr
e
ased SHARED_VERSION_IN
F
O to 6:0:0 (closing bug
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
R
oss
e
n Apostolov
Sm
a
ll cleanup of the openmm section i
n
md
r
un
.
c
commit
|
commitdiff
|
tree
2010-06-16
Ross
e
n Apostol
o
v
Merge b
r
anch 'ma
s
te
r
' of
git
.
g
r
omacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-16
Rossen Apostolov
Fixed
t
he co
m
mand line opt
i
ons f
o
r GPU binarie
s
.
commit
|
commitdiff
|
tree
2010-06-08
Rossen Apostol
o
v
Me
r
g
e
bra
n
ch 'mast
e
r' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-08
Rossen Apos
t
olov
A
d
d
ed miss
i
ng C-
t
e
rmi
n
al
o
xygens OC1 and OC2 to
the
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Rossen Apostolov
Is
s
ue a warning about using hardcoded O
B
C scale factors
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
R
ossen Apostol
o
v
OpenMM i
n
terface: issue a w
a
rning when the spec
i
fie
d
.
.
.
commit
|
commitdiff
|
tree
2010-05-14
Rossen Apostolov
The
r
elative
er
r
or
f
or cal
c
ulation
o
f Ewal
d
an
d
PME
.
.
.
commit
|
commitdiff
|
tree
2010-05-12
Rossen Apostolov
Merge branch
'mas
t
er'
o
f
g
i
t
.
g
r
omacs
.
org:
g
r
omacs
commit
|
commitdiff
|
tree
2010-05-12
Rossen Apostolov
Fix f
o
r Urey-Br
a
dley po
t
ent
i
al
in O
p
enMM
commit
|
commitdiff
|
tree
2010-05-11
Rossen Ap
o
stolov
A
d
ded suppo
r
t for Urey-Bradle
y
pot
e
n
t
ia
l
s
to the openmm
.
.
.
commit
|
commitdiff
|
tree
2010-05-04
Rossen Apostolov
Fixed
impro
p
e
r
error message in
o
p
e
nmm_wrapp
e
r
.
commit
|
commitdiff
|
tree
2010-04-01
Ros
s
en Apostolov
Minor fixes of typos
.
commit
|
commitdiff
|
tree
2010-03-31
R
ossen Apostolov
Fixed a gmx_warning crash in openmm_wra
p
per
.
c
p
p
commit
|
commitdiff
|
tree
2010-03-31
Rossen
A
p
ostolov
Fixed src
/
contri
b
/o
p
t
i
ons
.
c
to
u
se th
e
n
e
w pa
r
se_c
o
mmo
n
_
args
.
.
.
commit
|
commitdiff
|
tree
2010-03-27
Rossen Apostolov
OpenMM: "md" option
is now accepted
.
commit
|
commitdiff
|
tree
2010-03-24
Rossen Apostolov
Allowing also CUDA v
e
rsion
s
later
t
han 2
.
3
.
commit
|
commitdiff
|
tree
2010-03-24
Ro
s
s
e
n
Apostolov
Signal handling is
now e
n
abled for the
op
e
n
mm platform
.
commit
|
commitdiff
|
tree
2010-03-17
Rosse
n
A
postolov
o
penmm: some cl
e
a
nup in md_openmm
.
c and mdru
n
.
c
commit
|
commitdiff
|
tree
2010-03-12
Rossen A
p
o
stolov
Enabled c
h
eck
p
oints
in OpenMM
.
commit
|
commitdiff
|
tree
2010-03-12
Rossen Ap
o
stolov
Autom
a
tically dis
a
ble th
r
eads
for Open
M
M
bu
i
lds
.
commit
|
commitdiff
|
tree
2010-03-11
Ro
s
sen Apostolov
Vario
u
s fixes
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
S
m
all f
i
xes in mdrun desc
.
; enable periodic molecule
s
commit
|
commitdiff
|
tree
2010-03-11
Ro
s
sen Ap
o
stolov
Enal
b
ed
-ma
x
h op
t
ion for
u
sa
g
e with OpenMM
bi
n
aries
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostol
o
v
Cl
e
aned up do_md_
o
penmm
.
commit
|
commitdiff
|
tree
2010-03-11
R
o
s
s
en
A
postolov
Reworked
t
h
e
i
nte
g
rat
o
r and thermostat opti
o
ns
.
commit
|
commitdiff
|
tree
2010-03-11
R
ossen Apostolov
Fixed the
w
r
ong
output t
i
me frames
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apos
t
olov
do_md_opennmm
.
h
(aka pat
c
hed) now wor
k
s but the t
i
me
.
.
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
I
ni
t
i
a
l porting, do_md_op
e
nmm_nopatch
.
h is used
.
commit
|
commitdiff
|
tree
2009-10-02
Rossen
A
postolov
Us
e
rs are now refered to the new websi
t
e
i
n case
of
.
.
.
commit
|
commitdiff
|
tree
2009-08-17
Rossen
A
postol
o
v
Fixed incorrect s
c
al
i
ng of f
o
rces in
reciprocal
s
pace
.
.
.
commit
|
commitdiff
|
tree