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New release: 4.5 (final). Yay!!!
2010-09-01
R
o
ssen Apo
s
tolov
New
r
eleas
e
: 4
.
5
(
final)
.
Yay!!!
commit
|
commitdiff
|
tree
2010-09-01
Ros
s
en
A
postolov
Added g_rmsdist
and g_rotmat
to the
CM
a
ke build system
commit
|
commitdiff
|
tree
2010-09-01
Ro
s
sen
Apostolov
S
m
all
update
of the GPU related do
c
umen
t
a
tion
.
commit
|
commitdiff
|
tree
2010-09-01
R
o
ssen
A
postolov
Small update of the GPU r
e
la
t
ed documentati
o
n
.
commit
|
commitdiff
|
tree
2010-09-01
R
o
ss
e
n A
p
osto
l
o
v
Merge branch 'relea
s
e
-4-5-patches' of g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Ro
s
s
en Apostolov
M
erg
e
branc
h
'
r
e
l
ease-4-5-patches' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Rosse
n
A
p
ostolov
Mer
g
e branc
h
'release-4-5-
p
atc
h
es'
o
f git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
R
o
ss
e
n Apostolov
Ope
n
MM
now a
c
cepts
c
u
t
-o
f
f meth
o
d, since it'
s
needed
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
R
o
s
s
en A
p
ostolov
New rel
e
ase
4
.
5
-
beta4
commit
|
commitdiff
|
tree
2010-08-26
Ros
s
en Apostolov
M
o
di
f
ied the OpenMM wrapper int
e
rfac
e
to
suppor
t
the
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Rossen Apos
t
olov
Added the g_pme_error tool f
r
om
Florian D
o
mmert
.
Thanks!
commit
|
commitdiff
|
tree
2010-08-26
Ro
s
sen
A
postol
o
v
F
ixed har
d
co
d
e
d OpenMM
l
ib
r
ary name
.
commit
|
commitdiff
|
tree
2010-08-26
Ros
s
e
n Apos
t
olov
Re
m
oved the
u
nn
e
cessary hacks fr
o
m some boolean s
t
a
tements
.
commit
|
commitdiff
|
tree
2010-08-25
Rossen A
p
ostol
o
v
Rede
f
ine the
d
e
f
ault boolean type
to gmx_bool
.
commit
|
commitdiff
|
tree
2010-08-23
Rossen Aposto
l
o
v
Merge
bra
n
c
h 'release-4-5-patc
h
es' of git
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Rossen
A
posto
l
ov
Fixed a t
y
po about n
o
n-
e
x
i
sting macro in OpenMM
commit
|
commitdiff
|
tree
2010-08-19
Rossen Apostolov
Enable the Reference platform for O
p
e
nMM
.
commit
|
commitdiff
|
tree
2010-08-18
Ross
e
n Apostolov
M
e
rge branch
'release-4-5-pat
c
hes'
of git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Ross
e
n Apostolov
Fixed t
h
e exec
u
tio
n
o
rde
r
in OpenMM so that the generated
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen Ap
o
sto
l
ov
Preserve
t
he
.
pl extentions to
s
cripts
.
commit
|
commitdiff
|
tree
2010-08-16
Rossen A
p
ostolov
Removed the nb_kernel4xx_
i
ntel_syntax
.
c entr
i
e
s from
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Rossen Apostolov
Added suppo
r
t for i
m
proper dihed
r
als nee
d
ed for CHARMM
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Ro
s
sen Apostolov
OpenMM:
added supp
o
rt for
A
mberFF
p
rope
r
/impro
p
er torsion
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen Apostolov
Fix
e
d a reverted vers
i
o
n str
i
ng in
c
onf
i
g
u
r
e
.
ac
commit
|
commitdiff
|
tree
2010-08-12
R
o
ss
e
n Apo
s
tol
o
v
Merge b
r
anc
h
'release-4-5-patch
e
s'
of git
.
g
r
omac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Ro
s
sen
Apos
t
o
lov
Warnings about usi
n
g
broken
M
PI implementations
.
commit
|
commitdiff
|
tree
2010-08-12
R
o
ssen Ap
o
stolov
U
pdated the CMake
s
cripts for findi
n
g
CUDA, LibXml2
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Ro
s
sen Apostolov
Fixed broken linki
n
g with single pre
c
i
s
i
o
n fftw3 in
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen
Apostolov
Add
e
d
a
new fil
e
INSTAL
L
.
cmake with insta
l
l
a
tion
i
nst
r
uctio
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen
A
post
o
lov
Merge branch 'relea
s
e
-4-5-patches' of g
i
t
.
gro
m
acs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rosse
n
A
postolov
CMake builds now install GMXRC* fil
e
s
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen
A
postolov
Fix
f
o
r CM
a
k
e
bui
l
ds so
that they d
o
n
'
t f
a
il
eve
n
whe
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Rossen
A
po
s
tolo
v
Bumped vers
i
on
t
o 4
.
5-beta3
commit
|
commitdiff
|
tree
2010-08-10
Rossen Apostolov
Fixed a typo
i
n src/tools/CMakeLists
.
txt
.
commit
|
commitdiff
|
tree
2010-08-10
Ro
s
s
en
A
postolo
v
Adde
d
mi
s
sing
N
ULL in c
h
ain
s
ep enum i
n
pdb2gmx
.
commit
|
commitdiff
|
tree
2010-08-04
Rossen Apo
s
tolov
Fix share/html/o
n
line/mdp_opt
.
html
.
commit
|
commitdiff
|
tree
2010-08-04
Ro
s
sen Apo
s
tolov
F
i
xed configure
.
ac typo regrading
q
mmm-orca
.
commit
|
commitdiff
|
tree
2010-08-02
Rossen A
p
ostolov
N
ew bet
a
re
l
ease
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
Added
*
.
pc
.
cmakein
files for distribution
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apostolov
R
emov
e
d
O
penM
M
interface from
a
utoconf, use C
M
ake
ins
t
ead
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Ross
e
n
Aposto
l
ov
Fixed a typo in
p
r
evious Makef
i
le
.
am commit
commit
|
commitdiff
|
tree
2010-07-29
Rossen
Apostolov
Added f
o
r distr
i
b
u
tion some extr
a
files ne
e
ded by CMak
e
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen
A
postolov
Merge branch
'ma
s
ter'
o
f git
.
g
r
omac
s
.
o
r
g:gromac
s
commit
|
commitdiff
|
tree
2010-07-29
R
o
s
s
en Apostolo
v
Fixed typos in previo
u
s commit
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apost
o
lov
Add
e
d missing assembly files
in n
o
nbond
e
d/nb_kernel_
x
8
6
_64
_
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
R
ossen Apostolov
More mak
e
d
istcheck
f
ixes
.
commit
|
commitdiff
|
tree
2010-07-26
Rossen Apostolo
v
make
distc
h
e
c
k
fixe
s
commit
|
commitdiff
|
tree
2010-07-23
R
o
ssen Apos
t
o
lov
A
djust e
w
a
ld_rtol when passing it to Op
e
n
M
M
.
commit
|
commitdiff
|
tree
2010-07-21
Ro
s
sen
Apostolov
ew
a
ld_rtol
a
djustment for OpenMM
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
Ad
d
ed SHAR
E
D_VERSI
O
N_IN
F
O to libgm
x
p
reproc
e
ss
.
commit
|
commitdiff
|
tree
2010-07-20
R
ossen Apostolo
v
Moved the X11
a
ut
o
make de
p
endency flag ins
i
de ngmx
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
D
i
sabl
e
d adjus
t
m
ent of
ewald_rtol for OpenMM
.
commit
|
commitdiff
|
tree
2010-07-20
Rosse
n
Apostolov
By d
e
fault
G
MX_ACCELERATION
is now "auto"
.
commit
|
commitdiff
|
tree
2010-07-20
R
o
ssen Apostolov
Added support
for
O
p
enM
M
-2
.
0, and C
U
DA-3
.
1
is now req
u
ired
.
commit
|
commitdiff
|
tree
2010-07-02
Rossen Apostolov
Disab
l
e b
y
defa
u
lt ia64 assembly loops
.
Th
o
s
e
will
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Rossen Apostolov
M
erge branch 'm
a
ste
r
' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-02
Rossen
Apostolov
Dis
a
ble
A
l
lvsAll kernel
s
fo
r
very small
systems (<
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Rossen Apostolov
Initia
l
CTest
suppo
r
t
commit
|
commitdiff
|
tree
2010-06-23
Rossen Apo
s
t
o
lo
v
I
n
creased SHARE
D
_VERSION_
I
N
FO to 6:
0
:0 (closing bug
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Rossen Aposto
l
ov
Small
c
leanup of th
e
o
p
enmm section
i
n mdrun
.
c
commit
|
commitdiff
|
tree
2010-06-16
R
o
ssen Aposto
l
ov
Merge bran
c
h 'master
'
of git
.
gr
o
macs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-06-16
Rossen Apostolov
Fix
e
d t
h
e
c
o
mm
a
nd line
options
f
or G
P
U binar
i
es
.
commit
|
commitdiff
|
tree
2010-06-08
Rossen Apost
o
lov
Merge branch 'master' of git
.
grom
a
cs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-08
Rosse
n
Apost
o
lov
A
dded missin
g
C-ter
m
inal oxy
g
ens OC
1
a
n
d OC2
t
o the
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Rossen
A
p
o
stolov
Issue a warn
i
ng about
u
si
n
g
hardco
d
ed OBC scale factors
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
R
o
ssen
A
postolov
O
p
enMM interface: iss
u
e a war
n
ing when the specified
.
.
.
commit
|
commitdiff
|
tree
2010-05-14
Rossen Apostolov
The relative error f
o
r calcul
a
tion of Ewald and PM
E
.
.
.
commit
|
commitdiff
|
tree
2010-05-12
Rossen Apostolo
v
Merge branch '
m
aster'
o
f
git
.
gr
o
ma
c
s
.
o
rg:gromac
s
commit
|
commitdiff
|
tree
2010-05-12
Rossen Aposto
l
o
v
Fi
x
for Urey
-
Bradle
y
potential in OpenM
M
commit
|
commitdiff
|
tree
2010-05-11
Rossen Apostolov
Added support fo
r
Urey-Bradley po
t
enti
a
ls
to
the openmm
.
.
.
commit
|
commitdiff
|
tree
2010-05-04
Ross
e
n Apos
t
olov
Fixed improper error
message in openmm_wrapper
.
commit
|
commitdiff
|
tree
2010-04-01
Rossen Apostolov
Mi
n
or f
i
x
es of
typ
o
s
.
commit
|
commitdiff
|
tree
2010-03-31
Rossen Aposto
l
ov
Fi
x
ed a
g
mx_warnin
g
crash in openmm_wrapper
.
cpp
commit
|
commitdiff
|
tree
2010-03-31
Rossen Ap
o
stolov
Fixed src/contrib
/
options
.
c
to use the ne
w
parse_commo
n
_args
.
.
.
commit
|
commitdiff
|
tree
2010-03-27
R
o
ssen Apostolov
OpenMM: "md" option is now accepted
.
commit
|
commitdiff
|
tree
2010-03-24
Ros
s
en Apostolov
All
o
wing also CUDA versions later than
2
.
3
.
commit
|
commitdiff
|
tree
2010-03-24
Rossen Apostolov
Signal
h
a
n
dl
i
ng is now en
a
bled f
o
r the ope
n
m
m
platform
.
commit
|
commitdiff
|
tree
2010-03-17
Rossen A
p
ostolov
openm
m
: some cleanup in
md_openmm
.
c and mdrun
.
c
commit
|
commitdiff
|
tree
2010-03-12
R
o
ssen Apostolov
Enabled checkpoin
t
s in OpenMM
.
commit
|
commitdiff
|
tree
2010-03-12
Ross
e
n Apostol
o
v
Aut
o
matically di
s
able t
h
reads for OpenMM buil
d
s
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
Vario
u
s
f
ixes
.
commit
|
commitdiff
|
tree
2010-03-11
Ros
s
en
Apostolov
S
m
all fixes in mdrun desc
.
; enable pe
r
i
od
i
c mole
c
u
les
commit
|
commitdiff
|
tree
2010-03-11
Rosse
n
Apost
o
l
o
v
Enalbed -maxh
o
ption for us
a
ge
with OpenMM binaries
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apos
t
olov
Cleaned u
p
do_m
d
_o
p
enmm
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Ap
o
stolov
Rework
e
d the int
e
grator and t
h
ermostat
o
ptions
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen
A
p
ostol
o
v
Fixed the wrong out
p
ut tim
e
fra
m
e
s
commit
|
commitdiff
|
tree
2010-03-11
R
o
ssen Ap
o
stolov
do_md_opennmm
.
h (aka p
a
tched) now works but th
e
time
.
.
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen A
p
o
s
to
l
ov
Ini
t
ial port
i
ng, do_md_openmm_n
o
patch
.
h is used
.
commit
|
commitdiff
|
tree
2009-10-02
R
o
ssen Ap
o
s
t
olov
Users are now refered to the ne
w
web
s
ite
in case of
.
.
.
commit
|
commitdiff
|
tree
2009-08-17
Rossen Apostolov
Fixed inco
r
rect scaling of
f
orces
i
n recipro
c
al space
.
.
.
commit
|
commitdiff
|
tree