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New release: 4.5 (final). Yay!!!
2010-09-01
R
ossen Apostolov
New
r
elease: 4
.
5
(final)
.
Ya
y
!!!
commit
|
commitdiff
|
tree
2010-09-01
Rossen Apo
s
tolov
Added g_rmsdist and g_rotmat to t
h
e CMake bu
i
ld system
commit
|
commitdiff
|
tree
2010-09-01
Rossen Apos
t
olov
Sma
l
l updat
e
of the GP
U
relat
e
d
documentation
.
commit
|
commitdiff
|
tree
2010-09-01
R
o
ssen Apostolov
Sm
a
ll upd
a
te
o
f the GPU
r
ela
t
ed doc
u
mentation
.
commit
|
commitdiff
|
tree
2010-09-01
Rosse
n
Apostolo
v
Merge branch 'rele
a
se-4-5-patches' of gi
t
.
grom
a
cs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
R
o
ssen Ap
o
stolov
Merge branch 'release
-
4-5
-
p
a
tc
h
es' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Rossen Apost
o
l
ov
Me
r
g
e br
a
nch 'rel
e
ase-
4
-5-patches' of git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Rossen Apost
o
lov
OpenMM
now accepts cu
t
-off method, sin
c
e it's ne
e
de
d
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
R
o
ssen
A
posto
l
ov
New rele
a
se 4
.
5-beta4
commit
|
commitdiff
|
tree
2010-08-26
R
o
s
sen Apos
t
olov
Modified the
O
pe
n
M
M
wrapper
i
nterf
a
ce to
s
upport the
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Rossen Apostolov
Added t
h
e
g_
p
me_error to
o
l
from Fl
o
rian Dommert
.
T
h
a
nk
s
!
commit
|
commitdiff
|
tree
2010-08-26
Rossen
Ap
o
stolo
v
Fixed ha
r
dcoded OpenMM library
n
ame
.
commit
|
commitdiff
|
tree
2010-08-26
R
o
s
s
en Apostolov
Remov
e
d the unnecessary
h
a
cks f
r
om
s
ome boo
l
ean statements
.
commit
|
commitdiff
|
tree
2010-08-25
Rossen Apostolov
Redefine the
default
b
ool
e
an
t
yp
e
to gmx_bool
.
commit
|
commitdiff
|
tree
2010-08-23
Rossen Ap
o
stolov
Merge b
r
anch 're
l
ease-4-5-patches' of
g
it
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
R
o
ssen Apostolov
Fix
e
d
a typo ab
o
ut non
-
existing macr
o
in OpenMM
commit
|
commitdiff
|
tree
2010-08-19
Rossen Apostolo
v
Enable the Reference pla
t
form f
o
r
O
pen
M
M
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen Apostolov
Merge br
a
nch 'rel
e
ase-
4
-5-
p
a
t
ches
'
of
git
.
gr
o
macs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen Apost
o
l
o
v
Fixed the exe
c
u
tion order in OpenMM so that th
e
ge
n
erated
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen Apo
s
tolov
Pr
e
serve
t
he
.
pl extentions to scripts
.
commit
|
commitdiff
|
tree
2010-08-16
Rossen Apostolo
v
Re
m
oved
t
h
e nb_kernel4xx_int
e
l_syntax
.
c en
t
ri
e
s from
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Ross
e
n Apostolov
Added suppo
r
t
f
or im
p
r
o
p
er dihedrals needed for CHARM
M
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Ro
s
sen Apos
t
olov
OpenM
M
:
added support for AmberFF proper/
i
mproper
to
r
sion
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Ross
e
n Ap
o
s
tolov
F
ixed a reverted vers
i
on st
r
ing in co
n
f
i
gure
.
ac
commit
|
commitdiff
|
tree
2010-08-12
Rossen Apostolov
Mer
g
e branch 'release-4-5-patche
s
'
of git
.
gromac
s
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen A
p
ostolov
Warnings
a
bout usi
n
g broken MPI i
m
ple
m
ent
a
tions
.
commit
|
commitdiff
|
tree
2010-08-12
Ross
e
n Apostolov
Updated t
h
e CMak
e
scripts
f
or findin
g
C
U
DA
,
LibXml2
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apostolov
Fix
e
d
broken link
i
ng with single precision fftw3
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apost
o
lov
Added a ne
w
file
INSTA
L
L
.
cmake wi
t
h in
s
tal
l
atio
n
instructio
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apostolo
v
Merge branch 're
l
ea
s
e-4-5-patches
'
of g
i
t
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen
A
pos
t
olov
C
M
ak
e
bui
l
ds no
w
install
G
MXRC
*
fi
l
e
s
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apostolo
v
Fix for CMake b
u
ilds so that
t
hey don'
t
fail
even
w
hen
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Rosse
n
Apostolov
B
u
mped
ve
r
sion
t
o 4
.
5-beta3
commit
|
commitdiff
|
tree
2010-08-10
R
oss
e
n A
p
ostolov
Fixed a
typo
i
n
s
rc/tools/CMakeLists
.
txt
.
commit
|
commitdiff
|
tree
2010-08-10
Ros
s
en A
p
ostolo
v
Adde
d
missing N
U
L
L
in
chainsep
e
n
u
m
in pdb2gmx
.
commit
|
commitdiff
|
tree
2010-08-04
Ross
e
n Apostolov
F
i
x s
h
ar
e
/html/
o
nlin
e
/md
p
_opt
.
html
.
commit
|
commitdiff
|
tree
2010-08-04
Rossen Apos
t
o
lov
Fixed co
n
figur
e
.
ac typo regrading qmmm-orca
.
commit
|
commitdiff
|
tree
2010-08-02
Rossen Apostolov
New beta release
.
commit
|
commitdiff
|
tree
2010-07-29
Ro
s
sen Apostolov
Added *
.
pc
.
cmakein fil
e
s for dis
t
ribution
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
Removed OpenMM interface from autocon
f
, use CMake in
s
t
e
ad
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Ross
e
n Apos
t
o
l
ov
F
ixed a typo in previous Make
f
i
l
e
.
am
c
o
mmi
t
commit
|
commitdiff
|
tree
2010-07-29
Ros
s
en Apostolov
Added f
o
r d
i
stribution s
o
me extra files n
e
ede
d
by CMake
.
commit
|
commitdiff
|
tree
2010-07-29
Ro
s
sen Apostolov
M
e
r
g
e branch 'master' of git
.
gr
o
ma
c
s
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apo
s
tolov
F
i
x
ed ty
p
o
s in previous commit
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Aposto
l
o
v
Added
m
issing assem
b
ly
files in nonbonded/nb_kernel_
x
86_64_s
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Rossen
A
postolov
More make distcheck fixes
.
commit
|
commitdiff
|
tree
2010-07-26
Rossen A
p
ostolov
make distcheck fix
e
s
commit
|
commitdiff
|
tree
2010-07-23
R
o
ssen Apo
s
tolov
A
djust ewald_rtol when passing it to Open
M
M
.
commit
|
commitdiff
|
tree
2010-07-21
Rossen Apostolo
v
ewa
l
d_rtol
a
dju
s
tment for
O
penMM
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
Ad
d
ed
S
HARED_VERSION_INFO
to
libgmxpr
e
process
.
commit
|
commitdiff
|
tree
2010-07-20
Rosse
n
Aposto
l
ov
Moved the X11
a
uto
m
ake dependen
c
y
flag inside ngmx
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
Disabled adjus
t
ment of ewald
_
r
t
o
l
for OpenMM
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
By default GMX_ACCELERATION is now "auto
"
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
Added
s
upport for
O
pe
n
M
M-2
.
0,
a
nd C
U
DA-3
.
1
is now required
.
commit
|
commitdiff
|
tree
2010-07-02
Rossen Apostolov
Disa
b
le by default ia64 assembly loops
.
Those will
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
R
o
ssen Apost
o
lov
Merge
branc
h
'
m
aster
'
of git
.
g
r
o
m
acs
.
o
r
g
:
g
romacs
commit
|
commitdiff
|
tree
2010-07-02
Rossen Apostolov
Disab
l
e
All
v
sAll ker
n
e
ls for very
s
mall systems (<
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Rosse
n
Apostolov
Initial CT
e
st sup
p
ort
commit
|
commitdiff
|
tree
2010-06-23
Rossen
Apostolov
Incr
e
a
s
ed SHA
R
ED
_
VERS
I
ON_INFO to 6:0:
0
(closin
g
bug
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Rossen
A
posto
l
ov
Small
c
leanup of the ope
n
mm section in mdrun
.
c
commit
|
commitdiff
|
tree
2010-06-16
Rossen Apostol
o
v
M
erge branc
h
'
m
ast
e
r'
of git
.
gr
o
m
a
cs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-16
R
o
ssen Apostolov
F
i
xed th
e
c
o
mmand line options fo
r
GPU binari
e
s
.
commit
|
commitdiff
|
tree
2010-06-08
Rosse
n
A
p
ostolov
Merge branch 'master
'
of git
.
g
romacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-06-08
Rossen Apostolov
Added missing C
-
terminal ox
y
gens OC1 and O
C
2 to the
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Rossen Apostolo
v
Issu
e
a warni
n
g abo
u
t using hardcode
d
OBC scale
f
actors
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Ros
s
en Apostolov
Op
e
nMM interf
a
ce: issue
a
warning whe
n
the specifie
d
.
.
.
commit
|
commitdiff
|
tree
2010-05-14
Rossen Apostolo
v
The relative err
o
r for calcu
l
ation of
Ewald
a
nd PME
.
.
.
commit
|
commitdiff
|
tree
2010-05-12
Rossen Apostolov
Merge
bra
n
c
h
'master' of git
.
gromacs
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-05-12
Rossen
A
pos
t
olov
Fi
x
fo
r
Urey-Bradle
y
po
t
ential in OpenMM
commit
|
commitdiff
|
tree
2010-05-11
R
o
ssen Apostolov
A
dded support for Urey-B
r
adle
y
potentials to the open
m
m
.
.
.
commit
|
commitdiff
|
tree
2010-05-04
Rossen A
p
ostolov
Fixed
i
mproper error message in o
p
enmm_
w
rap
p
er
.
commit
|
commitdiff
|
tree
2010-04-01
Rossen Apostolov
Minor fixes
of typo
s
.
commit
|
commitdiff
|
tree
2010-03-31
R
o
ssen
A
postolov
Fixed a gmx_war
n
ing crash
i
n
o
penm
m
_wrapper
.
cpp
commit
|
commitdiff
|
tree
2010-03-31
Ro
s
sen Apostolov
F
i
xe
d
src/contrib
/
options
.
c to use
t
he
n
ew
par
s
e_commo
n
_args
.
.
.
commit
|
commitdiff
|
tree
2010-03-27
Ros
s
en Apo
s
tolov
Op
e
nMM:
"
md
"
option is n
o
w accep
t
ed
.
commit
|
commitdiff
|
tree
2010-03-24
Rossen Apostolov
All
o
wing also CUDA ver
s
ions later t
h
an 2
.
3
.
commit
|
commitdiff
|
tree
2010-03-24
Ros
s
en A
p
ostolov
Signal hand
l
i
n
g
is now enabled for the openmm p
l
atform
.
commit
|
commitdiff
|
tree
2010-03-17
Rossen Aposto
l
ov
openmm:
some c
l
ea
n
up in
md
_
openmm
.
c and md
r
u
n
.
c
commit
|
commitdiff
|
tree
2010-03-12
Rossen Ap
o
stolov
Enabl
e
d
c
h
eckpoin
t
s in
Ope
n
MM
.
commit
|
commitdiff
|
tree
2010-03-12
R
os
s
en Ap
o
s
tolov
Automatically disable threa
d
s for OpenMM buil
d
s
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
V
arious fi
x
es
.
commit
|
commitdiff
|
tree
2010-03-11
R
oss
e
n Apostolov
Smal
l
fi
x
es in mdru
n
desc
.
; e
n
able
perio
d
ic molecul
e
s
commit
|
commitdiff
|
tree
2010-03-11
Ross
e
n Apostol
o
v
Ena
l
bed -maxh option
f
or
usage with OpenMM binaries
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apos
t
o
lov
Cleaned up
do_md_openmm
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Ap
o
s
t
olov
Reworked the integrator
and t
h
ermostat options
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen
Apostolo
v
Fixe
d
the wrong output time f
r
a
mes
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
do_md_op
e
nnmm
.
h (aka pat
c
hed
)
now works but
t
he time
.
.
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
Initial porting, do_md_ope
n
mm_nop
a
t
ch
.
h is used
.
commit
|
commitdiff
|
tree
2009-10-02
Rossen Apostolov
Users are now r
e
fered to the
n
ew website in case o
f
.
.
.
commit
|
commitdiff
|
tree
2009-08-17
R
ossen Apostolov
F
ixed inco
r
rect s
c
aling of
f
orc
e
s
in rec
i
pr
o
ca
l
sp
a
c
e
.
.
.
commit
|
commitdiff
|
tree