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Warnings about using broken MPI implementations.
2010-08-12
Rossen Apostolov
War
n
i
ngs about usin
g
brok
e
n MPI imple
m
e
n
t
a
tion
s
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen Apos
t
olov
Updated th
e
CM
a
k
e s
c
rip
t
s
for finding CUDA, L
i
bXml2
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apostolov
Fixed broken linking with s
i
ng
l
e pr
e
cision fftw3
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
R
o
s
s
en Apos
t
olov
Added a new file
I
NSTALL
.
cmak
e
with installation i
n
structio
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
R
osse
n
Apostolov
Merge branch 'releas
e
-4-5-pat
c
hes' of
git
.
g
romacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apostolov
CMa
k
e bui
l
ds now install GMXR
C
*
f
iles
.
commit
|
commitdiff
|
tree
2010-08-11
Rosse
n
Apo
s
tolo
v
Fix fo
r
CMake bu
i
lds so that th
e
y don't fail even when
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Rossen Apos
t
olov
Bumped
version to 4
.
5
-
beta3
commit
|
commitdiff
|
tree
2010-08-10
R
ossen
Aposto
l
ov
Fixed a
typo in s
r
c/tools/
C
MakeLists
.
txt
.
commit
|
commitdiff
|
tree
2010-08-10
Rossen Apostolov
A
dded m
i
ssing NU
L
L
in
c
hain
s
ep enum in pdb2gmx
.
commit
|
commitdiff
|
tree
2010-08-04
Rossen A
p
o
s
t
olo
v
Fix sha
r
e/html/on
l
ine/md
p
_opt
.
htm
l
.
commit
|
commitdiff
|
tree
2010-08-04
Rossen
A
po
s
tolov
Fixed conf
i
gure
.
ac typo
reg
r
ading
q
mmm-orca
.
commit
|
commitdiff
|
tree
2010-08-02
Rossen Apostol
o
v
New beta
rel
e
ase
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Aposto
l
o
v
Added *
.
pc
.
cmakein files for distribu
t
ion
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
Removed
O
p
e
n
MM interface from aut
o
conf, use CMake instead
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Rosse
n
A
p
o
s
tolov
F
ixed
a
t
ypo
i
n
p
revious M
a
kefile
.
am
commit
commit
|
commitdiff
|
tree
2010-07-29
Rossen
A
postolov
Added for di
s
tributi
o
n s
o
me extr
a
files needed by
CMake
.
commit
|
commitdiff
|
tree
2010-07-29
R
o
ssen
Apostolov
Merge branc
h
'
m
aster' of git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-29
R
ossen
Apostolov
Fixed typos in
p
revious commit
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
Added
m
issing assem
b
ly f
i
les
in nonbo
n
ded
/
nb_kernel_x86_6
4
_
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
R
o
ssen Apostolov
M
ore mak
e
d
i
stcheck
fixes
.
commit
|
commitdiff
|
tree
2010-07-26
Ross
e
n Ap
o
sto
l
ov
ma
k
e d
i
s
tcheck fixes
commit
|
commitdiff
|
tree
2010-07-23
Rosse
n
Apost
o
lov
Ad
j
ust ew
a
l
d
_rtol
w
hen
p
assing
it to O
p
enMM
.
commit
|
commitdiff
|
tree
2010-07-21
Rossen Apostolov
ewald_r
t
ol adj
u
stment f
o
r Ope
n
M
M
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
A
d
d
e
d SHA
R
ED_
V
ERSI
O
N_INF
O
t
o
libgmxpre
p
roce
s
s
.
commit
|
commitdiff
|
tree
2010-07-20
R
o
ssen Apostolov
Mov
e
d the X11 auto
m
ake d
e
p
e
nd
e
ncy
f
lag inside ng
m
x
.
commit
|
commitdiff
|
tree
2010-07-20
Ro
s
sen Apostolov
D
isabled a
d
justme
n
t of ewald_rtol fo
r
OpenMM
.
commit
|
commitdiff
|
tree
2010-07-20
R
ossen
Apostolov
By default GM
X
_ACCELERATION is now "auto"
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Ap
o
stolov
Added support for
OpenMM-2
.
0,
and
C
UDA-3
.
1 is now
r
equired
.
commit
|
commitdiff
|
tree
2010-07-02
Rossen Apostolov
Di
s
a
b
le
by
d
efau
l
t
ia64 assembl
y
l
oops
.
Those will
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
R
o
ssen A
p
ostolov
Merg
e
bran
c
h 'maste
r
' of git
.
g
romacs
.
o
rg:gr
o
mac
s
commit
|
commitdiff
|
tree
2010-07-02
Rossen Apostolov
Di
s
a
ble AllvsAll kernels
for very small s
y
stems (<
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Rossen Aposto
l
ov
Initial
CTest support
commit
|
commitdiff
|
tree
2010-06-23
R
ossen
A
postolov
Inc
r
eased SHARED_VER
S
ION_
I
NFO to 6:0
:
0
(closin
g
bug
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Rossen Aposto
l
ov
Sma
l
l cleanup of the ope
n
m
m
section
in
m
drun
.
c
commit
|
commitdiff
|
tree
2010-06-16
Rossen Apostolov
Merge branch 'maste
r
' of git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-16
R
osse
n
Apostolov
Fixed the comman
d
l
i
ne
o
ptio
n
s
for
GP
U
binaries
.
commit
|
commitdiff
|
tree
2010-06-08
Rossen Apost
o
lov
Merge branch 'master' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-08
R
ossen A
p
ostolov
Added miss
i
ng C-termina
l
oxygen
s
OC1
and
OC2 to the
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Rossen
Apostolov
Issue a war
n
ing about us
i
ng
h
ardcoded
O
B
C
scale factors
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Ros
s
e
n
Apostolov
O
penMM i
n
t
e
r
face: issu
e
a war
n
ing
w
hen the sp
e
c
i
fied
.
.
.
commit
|
commitdiff
|
tree
2010-05-14
Rossen Apostolov
The relative erro
r
for c
a
lcula
t
ion of Ewald and PME
.
.
.
commit
|
commitdiff
|
tree
2010-05-12
Rossen
A
posto
l
ov
Merge
b
r
a
nc
h
'master' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-05-12
R
o
s
sen Apostolov
Fi
x
for Urey-
B
r
a
d
l
e
y potential in O
p
enMM
commit
|
commitdiff
|
tree
2010-05-11
Ros
s
en Apostolov
Added
support
for Urey-Bra
d
ley poten
t
ials t
o
th
e
openm
m
.
.
.
commit
|
commitdiff
|
tree
2010-05-04
Rossen
A
postolov
Fixed improper
e
rror m
e
ss
a
ge in openmm_
w
rapper
.
commit
|
commitdiff
|
tree
2010-04-01
Ross
e
n Apost
o
lov
Mino
r
f
ixes of ty
p
o
s
.
commit
|
commitdiff
|
tree
2010-03-31
Rossen A
p
ostolov
Fi
x
ed a gmx_warni
n
g cras
h
i
n
openmm_
w
rapper
.
cpp
commit
|
commitdiff
|
tree
2010-03-31
Rossen Apostolov
Fixed
s
r
c
/contrib/options
.
c t
o
u
s
e t
h
e new par
s
e_commo
n
_arg
s
.
.
.
commit
|
commitdiff
|
tree
2010-03-27
Rosse
n
Apostolov
OpenMM: "md
"
option i
s
now accepted
.
commit
|
commitdiff
|
tree
2010-03-24
Rossen Apostolov
Allo
w
i
ng also CUDA v
e
rsi
o
ns later than 2
.
3
.
commit
|
commitdiff
|
tree
2010-03-24
Rossen Apostolov
Si
g
nal
handl
i
n
g
is now enab
l
ed for the
o
pen
m
m pl
a
t
form
.
commit
|
commitdiff
|
tree
2010-03-17
R
ossen
Apo
s
tolov
open
m
m
: s
o
me
cle
a
nup in md_op
e
nmm
.
c a
n
d mdrun
.
c
commit
|
commitdiff
|
tree
2010-03-12
R
o
ssen Apostolov
Enabled
c
heckpoints in
O
p
e
nMM
.
commit
|
commitdiff
|
tree
2010-03-12
Ross
e
n
Apostolov
Automa
t
ically disabl
e
threads
f
o
r
OpenMM builds
.
commit
|
commitdiff
|
tree
2010-03-11
Ros
s
en
A
p
os
t
o
l
o
v
V
a
riou
s
f
i
xes
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
Small fix
e
s i
n
mdrun des
c
.
; enable periodic molecu
l
es
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
Enalbed -maxh o
p
tion for usage with OpenMM binaries
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
Cleaned up
do_md_openmm
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
Reworked
the integrator and thermostat o
p
tions
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apost
o
lov
Fixe
d
the wrong output time
f
rames
commit
|
commitdiff
|
tree
2010-03-11
R
ossen Apostolov
do_md_ope
n
n
mm
.
h (aka patched)
n
ow works but the time
.
.
.
commit
|
commitdiff
|
tree
2010-03-11
Ros
s
en Apostol
o
v
Initial
p
ortin
g
,
d
o
_md_o
p
e
nmm
_
nopatch
.
h i
s
used
.
commit
|
commitdiff
|
tree
2009-10-02
Rossen
Apostolov
U
s
e
r
s
a
re now refered to the new
w
ebsite in case of
.
.
.
commit
|
commitdiff
|
tree
2009-08-17
Rossen Apostolov
Fixed incorrect scaling of fo
r
c
e
s in recip
r
ocal space
.
.
.
commit
|
commitdiff
|
tree