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New release: 4.5 (final). Yay!!!
2010-09-01
Ro
s
sen Apostolov
New release: 4
.
5 (fi
n
al)
.
Y
ay!!!
commit
|
commitdiff
|
tree
2010-09-01
Rosse
n
Aposto
l
ov
Add
e
d g_rmsd
i
s
t and g_rotmat to
t
he
C
Make build system
commit
|
commitdiff
|
tree
2010-09-01
Ro
s
sen Apos
t
olov
S
m
all
u
pda
t
e of the G
P
U related
documentati
o
n
.
commit
|
commitdiff
|
tree
2010-09-01
Rossen Apostolov
Small update of t
h
e GPU rel
a
ted
d
o
cumentation
.
commit
|
commitdiff
|
tree
2010-09-01
Rossen Apo
s
tolo
v
M
erge
branch 'releas
e
-4-5-pa
t
c
h
es' of git
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Rossen Apostol
o
v
Merge br
a
nch '
r
elease-4-5-patches' o
f
gi
t
.
gro
m
acs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Ross
e
n
Apostol
o
v
Merge
b
ranch 'relea
s
e-4-5-p
a
tches'
o
f
g
i
t
.
g
rom
a
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Rossen
Apostolov
O
penMM now accepts cut-off method, since it's needed
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Rossen Apostolov
N
e
w relea
s
e 4
.
5
-
beta4
commit
|
commitdiff
|
tree
2010-08-26
Rossen
A
postolov
Modified the OpenMM wrapp
e
r
i
nterface t
o
support
t
h
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
R
o
ssen Apostolov
Added the g_pme_e
r
ror too
l
from F
l
orian Domm
e
rt
.
Thank
s
!
commit
|
commitdiff
|
tree
2010-08-26
Rossen Apost
o
l
o
v
Fix
e
d hardcoded Op
e
nM
M
library
n
ame
.
commit
|
commitdiff
|
tree
2010-08-26
R
ossen Apostol
o
v
Removed
t
he unnecessary hacks from
s
ome boolean s
t
atements
.
commit
|
commitdiff
|
tree
2010-08-25
R
os
s
en Apostolov
R
e
de
f
ine the
defau
l
t boo
l
ean t
y
pe
t
o
gmx_bo
o
l
.
commit
|
commitdiff
|
tree
2010-08-23
Rossen Apostolov
Merge branch
'rel
e
ase-4
-
5-patch
e
s' of
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Rossen
A
postolov
Fi
x
ed a typo about non-exis
t
ing
macro in OpenMM
commit
|
commitdiff
|
tree
2010-08-19
R
o
ssen Apostolov
Enable the
R
eferen
c
e pla
t
for
m
for OpenMM
.
commit
|
commitdiff
|
tree
2010-08-18
Ros
s
e
n Apostolov
Merge
b
ranch
'release-4-5-patches' of git
.
g
r
o
m
a
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
R
o
sse
n
Apostolov
Fixed the
execution orde
r
in OpenMM so th
a
t
the g
e
ner
a
ted
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen
Apostolov
P
rese
r
ve th
e
.
pl ext
e
n
tions to scr
i
pts
.
commit
|
commitdiff
|
tree
2010-08-16
Ro
s
s
e
n
Apos
t
ol
o
v
Re
m
ove
d
the nb_kernel4xx
_
inte
l
_syn
t
ax
.
c entries from
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Rosse
n
Apostolov
Added suppo
r
t
f
o
r improper
d
ihe
d
rals neede
d
for CHA
R
M
M
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen Apostolov
OpenMM:
a
dded support for AmberFF proper/imprope
r
torsi
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Rosse
n
Apostolov
Fixed a reve
r
t
e
d ve
r
sion string in
configure
.
ac
commit
|
commitdiff
|
tree
2010-08-12
R
o
ssen Apostolov
Merge
b
ranch 'releas
e
-4-5-patches' of gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Ro
s
sen Apos
t
olov
War
n
in
g
s abou
t
using br
o
k
en MPI
imple
m
enta
t
ions
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen A
p
o
s
t
olov
Up
d
a
t
ed the CMake scripts for finding CUDA, LibXml2
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apostolov
Fixed broke
n
linking with s
i
ngle
p
recision
f
f
tw
3
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen
Apostolov
Adde
d
a
n
ew file INSTALL
.
cmake with installa
t
i
o
n
i
nstructio
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen
Apostolov
Merge br
a
nch 'rel
e
ase
-
4-5-pat
c
hes' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen A
p
ostolov
CMake builds
n
ow in
s
ta
l
l GMXRC* files
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen
Apos
t
o
lov
F
i
x for CMake builds so that th
e
y don't fail e
v
en when
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Rossen Apost
o
lo
v
Bumped version to 4
.
5-beta3
commit
|
commitdiff
|
tree
2010-08-10
Rosse
n
Apos
t
olo
v
F
i
xed a typo in src/tools
/
CMakeLists
.
txt
.
commit
|
commitdiff
|
tree
2010-08-10
Rossen Apostolov
Added missing NULL in chainsep enu
m
in pdb2gmx
.
commit
|
commitdiff
|
tree
2010-08-04
Ross
e
n Apostolov
Fix share/html/online/m
d
p_o
p
t
.
html
.
commit
|
commitdiff
|
tree
2010-08-04
R
o
ssen
Apos
t
olov
Fixed
configure
.
a
c typo re
g
radin
g
qmmm-or
c
a
.
commit
|
commitdiff
|
tree
2010-08-02
R
o
s
sen Apostolov
N
ew beta release
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
Added *
.
pc
.
cmak
e
i
n
f
i
les for distribution
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apos
t
o
lov
Removed Ope
n
MM i
n
te
r
fa
c
e
fro
m
a
u
t
oconf,
use CMake in
s
tead
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Aposto
l
ov
Fixed
a
typo i
n
previous Makefi
l
e
.
a
m
commit
commit
|
commitdiff
|
tree
2010-07-29
Ros
s
en Apostolov
Added for distri
b
ution some extra files needed by CMake
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen A
p
ostolov
Merge br
a
nch 'master' of git
.
gromacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2010-07-29
Rossen
Apostolov
F
i
xed typ
o
s in previous commit
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
Added missing
a
ssembly fi
l
es in nonbonded/
n
b
_kernel_x86_64_s
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Ros
s
en
Apo
s
tolov
More make
distc
h
eck fixes
.
commit
|
commitdiff
|
tree
2010-07-26
Rossen A
p
ostolov
make di
s
tcheck fixes
commit
|
commitdiff
|
tree
2010-07-23
Ross
e
n Apos
t
olov
Adjust ewald
_
rtol when passing it to Open
M
M
.
commit
|
commitdiff
|
tree
2010-07-21
Ro
s
sen Apostolov
e
w
ald_r
t
ol
a
djus
t
ment fo
r
OpenMM
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Ap
o
stolov
Added SHARED_VE
R
SION_I
N
F
O
t
o
libgmxprepr
o
cess
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
Moved
t
he
X
11 au
t
omake dependency f
l
ag
i
nside ngmx
.
commit
|
commitdiff
|
tree
2010-07-20
Ros
s
en Apostolov
Disab
l
ed adjustment of ewald_r
t
ol for Ope
n
MM
.
commit
|
commitdiff
|
tree
2010-07-20
Ros
s
en Aposto
l
ov
By default
G
M
X_ACCELERATIO
N
is
now "auto
"
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
A
dded suppo
r
t for OpenMM-2
.
0
, and CUDA-3
.
1 is now required
.
commit
|
commitdiff
|
tree
2010-07-02
R
o
ssen
Apo
s
tolov
Disable by default ia64 as
s
embly loops
.
Those will
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Rossen
A
postolov
M
e
rge br
a
nch 'maste
r
'
of git
.
g
r
omacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-07-02
R
oss
e
n Apostolov
D
i
sable A
l
lvsAll kernels
fo
r
ver
y
sma
l
l system
s
(<
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Rossen Apostolov
Initial CTe
s
t
support
commit
|
commitdiff
|
tree
2010-06-23
Rossen A
p
ostolov
Increased SHARE
D
_VERS
I
ON_INFO to 6:0:0
(closing
b
u
g
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Rossen Apostolov
Small cle
a
nup
o
f
the openmm section in mdrun
.
c
commit
|
commitdiff
|
tree
2010-06-16
Rossen Apostol
o
v
Merge
b
ranch 'master'
of
git
.
gromacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-06-16
Ross
e
n
A
postolov
Fix
e
d
t
he command line optio
n
s
for GPU binaries
.
commit
|
commitdiff
|
tree
2010-06-08
Ross
e
n Apostolov
Merg
e
bran
c
h '
m
aster'
o
f
g
it
.
gro
m
acs
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-06-08
Rossen
Apostolov
Added mis
s
i
ng C-ter
m
inal oxyge
n
s
OC1 and OC
2
to the
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Rossen
A
posto
l
ov
Issue a wa
r
ning ab
o
ut
using har
d
cod
e
d
O
BC
s
cale factors
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Rossen A
p
ostolo
v
Open
M
M interface: issue a warnin
g
when the specifie
d
.
.
.
commit
|
commitdiff
|
tree
2010-05-14
R
o
s
sen A
p
ostolov
The
r
elati
v
e
error for calculation of Ewald and
P
M
E
.
.
.
commit
|
commitdiff
|
tree
2010-05-12
R
ossen
A
postol
o
v
M
erge branch 'mast
e
r' of gi
t
.
gromacs
.
o
rg:
g
romacs
commit
|
commitdiff
|
tree
2010-05-12
Ro
s
sen Apostolov
Fix
for Urey-Bradley
p
otential
in OpenMM
commit
|
commitdiff
|
tree
2010-05-11
Ro
s
s
e
n Apostolov
Added su
p
port for U
r
ey-Bra
d
ley potentials
to the ope
n
mm
.
.
.
commit
|
commitdiff
|
tree
2010-05-04
Rossen Apostolov
Fixe
d
improper error mes
s
age in
o
penmm_wrapper
.
commit
|
commitdiff
|
tree
2010-04-01
R
ossen Apostolov
Minor fixes of typos
.
commit
|
commitdiff
|
tree
2010-03-31
Rossen Apos
t
olov
Fixed a gmx_
w
arning cras
h
i
n
open
m
m_wrapper
.
cpp
commit
|
commitdiff
|
tree
2010-03-31
Rossen Apostolo
v
Fixe
d
src
/
contr
i
b/options
.
c to use the new parse_comm
o
n_
a
rgs
.
.
.
commit
|
commitdiff
|
tree
2010-03-27
R
ossen
A
postolo
v
OpenMM: "md
"
option is n
o
w accepte
d
.
commit
|
commitdiff
|
tree
2010-03-24
Rosse
n
Apostolov
A
llowi
n
g also CU
D
A versio
n
s later than 2
.
3
.
commit
|
commitdiff
|
tree
2010-03-24
Rossen Apostolov
Signal handling
is now enabled f
o
r th
e
openm
m
p
l
a
tform
.
commit
|
commitdiff
|
tree
2010-03-17
Rossen Ap
o
stol
o
v
openmm:
some cleanu
p
in md_openmm
.
c and mdrun
.
c
commit
|
commitdiff
|
tree
2010-03-12
Rossen Apo
s
to
l
o
v
Ena
b
led check
p
oin
t
s
i
n OpenMM
.
commit
|
commitdiff
|
tree
2010-03-12
Rossen Apostolov
Autom
a
tically
d
isable threads for OpenMM builds
.
commit
|
commitdiff
|
tree
2010-03-11
R
o
s
sen Ap
o
stolov
Various
f
ixes
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
Small
f
ixes
i
n mdru
n
des
c
.
; e
n
able periodic molecules
commit
|
commitdiff
|
tree
2010-03-11
Ros
s
en Apostolov
Enalb
e
d -maxh option for usage with O
p
enM
M
b
i
n
a
ri
e
s
commit
|
commitdiff
|
tree
2010-03-11
R
o
ssen Apos
t
olov
Cleaned up do_md_
o
penmm
.
commit
|
commitdiff
|
tree
2010-03-11
Ros
s
e
n Apostolov
Reworke
d
the integrat
o
r and therm
o
stat option
s
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
Fi
x
ed the wron
g
output time frames
commit
|
commitdiff
|
tree
2010-03-11
Ross
e
n
A
post
o
lov
do_md_o
p
e
nnm
m
.
h
(a
k
a patched) now works but the time
.
.
.
commit
|
commitdiff
|
tree
2010-03-11
Ros
s
en Ap
o
stolov
Initia
l
porting,
do
_
md_openmm_nopatch
.
h
i
s used
.
commit
|
commitdiff
|
tree
2009-10-02
Rossen Ap
o
stol
o
v
Users are n
o
w refered to the new website in ca
s
e o
f
.
.
.
commit
|
commitdiff
|
tree
2009-08-17
Rossen
A
post
o
lov
Fixed
i
ncorrect scal
i
n
g
of force
s
i
n re
c
i
proc
a
l sp
a
ce
.
.
.
commit
|
commitdiff
|
tree