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Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
2010-08-23
Ro
s
sen Apos
t
olov
Merge branch 'release-4-5-pa
t
ches'
of git
.
g
r
omac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Rossen
A
p
ostol
o
v
Fixed
a typo about non
-
existing
m
acro in O
p
enMM
commit
|
commitdiff
|
tree
2010-08-19
Ros
s
en Apostolov
Enable the Re
f
e
r
ence
platform for OpenMM
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen Apo
s
tolov
Merge branch 'release-4-5-pa
t
ch
e
s' of g
i
t
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen Apo
s
t
olov
Fixed the execution order in O
p
e
n
MM so that the gener
a
ted
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen Ap
o
stolov
Preser
v
e the
.
p
l extentions to s
c
ript
s
.
commit
|
commitdiff
|
tree
2010-08-16
R
oss
e
n Apostolov
Removed the nb_kernel4xx_int
e
l
_
syn
t
ax
.
c en
t
ri
e
s
f
rom
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Rosse
n
A
p
ostolov
Adde
d
sup
p
ort for impro
p
er
d
ihedrals needed for CHARMM
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen Apost
o
lov
OpenMM
:
added support for Amber
F
F prope
r
/
improper torsion
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen Apostolov
Fixed
a
rev
e
rted v
e
rs
i
o
n string in
c
on
f
i
gure
.
ac
commit
|
commitdiff
|
tree
2010-08-12
Ro
s
sen A
p
ostolov
Merge branch 'release-4-
5
-pa
t
c
h
es'
of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Ro
s
se
n
A
p
ostolov
Warnings
about
u
s
i
n
g
broken MPI implementations
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen A
p
ostol
o
v
Updated the CMake scripts
f
o
r
fi
n
ding CUDA, LibXml2
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Ross
e
n Apostolov
Fixed broken l
i
nking
w
ith single
p
recision fftw3
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apostolov
Added a new file INSTALL
.
cmake
with i
n
stallation instructio
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apo
s
t
o
lo
v
Merge branch 'release-4-5-pat
c
h
es' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apostolov
C
Make builds now ins
t
a
l
l
GMXRC*
files
.
commit
|
commitdiff
|
tree
2010-08-11
Rosse
n
Apostolov
Fi
x
for
CMake build
s
so that t
h
ey don't fail
even when
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Rossen Apostol
o
v
Bum
p
ed version to 4
.
5
-
beta3
commit
|
commitdiff
|
tree
2010-08-10
Rossen
A
postolov
Fixed a typo i
n
src/tools/
C
M
akeLists
.
t
xt
.
commit
|
commitdiff
|
tree
2010-08-10
Rossen Ap
o
s
tolov
A
d
ded missing NULL in chainsep enum in pdb2gmx
.
commit
|
commitdiff
|
tree
2010-08-04
Rossen Apost
o
lov
Fi
x
sh
a
re/
h
t
ml/online/mdp_
o
pt
.
ht
m
l
.
commit
|
commitdiff
|
tree
2010-08-04
R
ossen Apostolov
Fixe
d
configure
.
ac t
y
po regrading q
m
mm-orca
.
commit
|
commitdiff
|
tree
2010-08-02
Rossen
A
p
o
s
tolov
New beta release
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
Add
e
d *
.
pc
.
cm
a
kein files for
d
i
s
tribution
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostol
o
v
Removed
O
penMM i
n
ter
f
ace fr
o
m autoconf,
u
se C
M
ake in
s
tead
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apos
t
olov
Fixed a typo
in previou
s
Makefile
.
am commi
t
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
Added for dis
t
ribution some e
x
tra f
i
l
e
s needed by CMake
.
commit
|
commitdiff
|
tree
2010-07-29
Rosse
n
Apostolov
Mer
g
e branch
'
master' of git
.
gromacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apo
s
tolov
Fi
x
ed typos
i
n
previous commit
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Ap
o
stolov
Adde
d
mis
s
ing assembly files in non
b
onded/nb_k
e
rnel_x86
_
64_s
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Rossen Apostolov
More make dis
t
check fixes
.
commit
|
commitdiff
|
tree
2010-07-26
R
os
s
en Ap
o
stolov
ma
k
e dis
t
check fixes
commit
|
commitdiff
|
tree
2010-07-23
Rossen Apo
s
tolov
Adjust ewald
_
rtol
w
hen
p
assing it to OpenM
M
.
commit
|
commitdiff
|
tree
2010-07-21
Rossen
Apos
t
olov
ewal
d
_
rtol
a
djustment for Ope
n
MM
.
commit
|
commitdiff
|
tree
2010-07-20
Ro
s
sen Apostolov
Added SHARED_VERSION_INF
O
to li
b
gmx
p
reprocess
.
commit
|
commitdiff
|
tree
2010-07-20
R
ossen Apostolo
v
Moved the X11 auto
m
ake dep
e
ndency flag
i
nside ngmx
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen
Apostolov
Disab
l
ed adju
s
tment of ewal
d
_rtol f
o
r
O
p
enMM
.
commit
|
commitdiff
|
tree
2010-07-20
Ros
s
en Apostolov
By default GM
X
_ACCELERAT
I
ON is now "
a
u
to"
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen A
p
ostolov
Added
s
upport for OpenM
M
-2
.
0, and C
U
DA-3
.
1 is now requir
e
d
.
commit
|
commitdiff
|
tree
2010-07-02
R
ossen A
p
os
t
olov
D
i
sable b
y
d
e
f
ault
ia64 assembly loops
.
Those will
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Rossen Apos
t
olo
v
Me
r
ge branch
'
master' o
f
git
.
gromacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-07-02
Rossen Apostol
o
v
Disable
AllvsA
l
l kerne
l
s
f
o
r v
e
ry sma
l
l systems
(
<
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
R
o
ssen A
p
os
t
olov
Initial
C
T
e
st sup
p
ort
commit
|
commitdiff
|
tree
2010-06-23
Ross
e
n Apo
s
tolov
Increase
d
S
H
ARED_VERSI
O
N_INFO to 6:0:0
(
closing
bug
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Ros
s
en Apostolov
Small cleanup of the ope
n
mm section
i
n mdru
n
.
c
commit
|
commitdiff
|
tree
2010-06-16
Rossen Apostolov
Merge branch
'master' of git
.
grom
a
cs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-16
Rossen Apo
s
tolov
Fixed the
c
omma
n
d line options for GPU
b
i
naries
.
commit
|
commitdiff
|
tree
2010-06-08
Rossen Apostolov
Merg
e
b
r
anc
h
'master' of git
.
gr
o
m
acs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-08
Rossen Ap
o
stol
o
v
A
dded m
i
ssin
g
C-te
r
mi
n
al
o
xyg
e
ns OC1 and OC2 to t
h
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Ro
s
s
en Apos
t
olov
Issue a
w
a
rning
ab
o
ut using h
a
rdcoded OBC sca
l
e factors
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Ro
s
sen Apostolov
OpenMM int
e
r
face: issue
a
w
a
rn
i
ng
w
hen the s
p
ec
i
fied
.
.
.
commit
|
commitdiff
|
tree
2010-05-14
Rossen Apostolov
The relative e
r
ror for calc
u
lation
of Ew
a
ld and
PME
.
.
.
commit
|
commitdiff
|
tree
2010-05-12
Ross
e
n Apostolov
M
erge branc
h
'master' of git
.
gro
m
acs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-05-12
Rossen Apostolov
Fix f
o
r Urey
-
Bra
d
ley potenti
a
l in OpenMM
commit
|
commitdiff
|
tree
2010-05-11
Rossen Apostolov
Added support for Urey-Bradle
y
po
t
entia
l
s to the
openmm
.
.
.
commit
|
commitdiff
|
tree
2010-05-04
Rossen Apostol
o
v
F
i
xed impro
p
er error
m
essage in openmm_wrapper
.
commit
|
commitdiff
|
tree
2010-04-01
Rossen Apostolov
Minor fixes of
typos
.
commit
|
commitdiff
|
tree
2010-03-31
R
ossen Apos
t
o
lov
Fixed a gmx_
w
arning cra
s
h
in openmm_wrappe
r
.
cpp
commit
|
commitdiff
|
tree
2010-03-31
Rossen Apostolov
Fixed s
r
c/
c
ontr
i
b/optio
n
s
.
c to use the ne
w
p
arse_comm
o
n_args
.
.
.
commit
|
commitdiff
|
tree
2010-03-27
R
ossen Apostolo
v
Ope
n
MM: "md
"
o
p
tion is now accepted
.
commit
|
commitdiff
|
tree
2010-03-24
Rosse
n
Apo
s
tol
o
v
Allowing a
l
so CUDA versions later than
2
.
3
.
commit
|
commitdiff
|
tree
2010-03-24
Rossen Apos
t
olov
Signal handling is now
ena
b
led
for the
openmm pl
a
tform
.
commit
|
commitdiff
|
tree
2010-03-17
R
o
s
sen Ap
o
stolo
v
openm
m
:
s
ome clea
n
up in md_openmm
.
c a
n
d
m
d
r
u
n
.
c
commit
|
commitdiff
|
tree
2010-03-12
Ross
e
n Apostolov
E
n
abled che
c
kpoints
i
n OpenMM
.
commit
|
commitdiff
|
tree
2010-03-12
Rossen
Ap
o
stolov
Automatical
l
y disa
b
le threads for Op
e
nMM bu
i
lds
.
commit
|
commitdiff
|
tree
2010-03-11
Ross
e
n Apos
t
olov
Various fixes
.
commit
|
commitdiff
|
tree
2010-03-11
R
ossen
A
postolov
Small fixes in mdr
u
n desc
.
;
e
nable perio
d
ic molecu
l
es
commit
|
commitdiff
|
tree
2010-03-11
Szila
r
d Pall
OpenMM
b
uil
d
not de
p
e
n
de
n
t
o
n f
f
tw anymore
commit
|
commitdiff
|
tree
2010-03-11
Szilard
P
all
fixed
mdrun verbosity with
OpenMM build
commit
|
commitdiff
|
tree
2010-03-11
Szilar
d
Pall
f
ix
e
d a missing comma and a typo
i
n ope
n
mm_wrapper
commit
|
commitdiff
|
tree
2010-03-11
Ro
s
s
e
n
A
posto
l
o
v
Enalbed -maxh op
t
ion
for usage with
O
penMM
b
inaries
commit
|
commitdiff
|
tree
2010-03-11
R
ossen Apostolov
Clean
e
d up do_md_openmm
.
commit
|
commitdiff
|
tree
2010-03-11
Szilard Pall
D
e
lete src/kernel/do_md_openm
m
_nopat
c
h
.
h
, it
'
s not
.
.
.
commit
|
commitdiff
|
tree
2010-03-11
Sz
i
l
a
r
d
P
all
Minor cleanu
p
,
s
om
e
rearrangaments, and commenting
.
commit
|
commitdiff
|
tree
2010-03-11
Szilar
d
Pall
Reverted stu
p
id change i
n
CMal
e
Lists
.
tx
t
commit
|
commitdiff
|
tree
2010-03-11
Szil
a
rd Pall
Renamed md_openmm into openmm_wrapper,
and do
_
md_
o
penmm
.
.
.
commit
|
commitdiff
|
tree
2010-03-11
Ros
s
en Apost
o
l
o
v
Reworked t
h
e inte
g
rator and
thermostat options
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apos
t
olov
Fixed the
wrong out
p
u
t
t
im
e
frames
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apo
s
tolov
do_m
d
_
o
penn
m
m
.
h (aka patched)
n
ow works but the time
.
.
.
commit
|
commitdiff
|
tree
2010-03-11
Rosse
n
Apostolov
Initia
l
porting, do_m
d
_o
p
enmm_nopatch
.
h i
s
used
.
commit
|
commitdiff
|
tree
2009-10-02
R
o
ssen Apostolov
U
s
er
s
are now refered to the new
w
e
bsi
t
e
i
n case
of
.
.
.
commit
|
commitdiff
|
tree
2009-08-17
Ro
s
s
e
n Apostolov
Fixed
i
n
correct scalin
g
of forces in reci
p
rocal sp
a
ce
.
.
.
commit
|
commitdiff
|
tree