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OpenMM now accepts cut-off method, since it's needed for implicit solvent calculations.
2010-08-31
Ros
s
en Apostolov
OpenMM no
w
accepts cut-of
f
met
h
o
d
, si
n
ce
it
'
s
needed
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Rosse
n
Apostolov
N
ew release 4
.
5
-
be
t
a4
commit
|
commitdiff
|
tree
2010-08-26
Ross
e
n Apostolov
Modifie
d
the OpenMM wrapper inte
r
face
t
o support the
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Rossen A
p
ostolov
A
d
ded the g_
p
me_error to
o
l fro
m
Florian
Dom
m
ert
.
T
han
k
s!
commit
|
commitdiff
|
tree
2010-08-26
R
o
ssen Aposto
l
o
v
F
i
x
e
d
h
ardcoded OpenMM library name
.
commit
|
commitdiff
|
tree
2010-08-26
R
ossen
Apo
s
tolo
v
Re
m
oved the unnecessar
y
hacks
from som
e
boolean
s
t
a
t
em
e
nts
.
commit
|
commitdiff
|
tree
2010-08-25
Ro
s
sen Apostol
o
v
R
e
d
efine the default b
o
olean
t
ype to gmx_bool
.
commit
|
commitdiff
|
tree
2010-08-23
Ro
s
sen A
p
ostolo
v
Merge
b
ran
c
h '
r
elea
s
e-4-
5
-patche
s
'
o
f
g
it
.
g
roma
c
s
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Rossen Apostolov
Fi
x
ed a t
y
po about
non-existin
g
macro
i
n
OpenMM
commit
|
commitdiff
|
tree
2010-08-19
Rossen Apostolov
Enable the
R
efere
n
ce
pl
a
t
form f
o
r OpenMM
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen Apos
t
olov
Merge branch 'release-4-5-p
a
tches'
o
f git
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
R
ossen A
p
ostolov
F
ixed
t
he execution o
r
der i
n
OpenMM s
o
t
h
a
t
th
e
ge
n
erated
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen
A
postolo
v
Prese
r
ve th
e
.
pl extentions to scripts
.
commit
|
commitdiff
|
tree
2010-08-16
Rossen Apostolov
Rem
o
ved the
nb_
k
ernel4xx_inte
l
_syntax
.
c entri
e
s from
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Rosse
n
A
p
osto
l
ov
Adde
d
support
for impro
p
er dihe
d
r
a
ls needed for CHARMM
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen Apostol
o
v
OpenM
M
:
added support for AmberFF proper/improp
e
r torsi
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen Ap
o
s
t
o
l
ov
Fixed a reverted version strin
g
in configure
.
ac
commit
|
commitdiff
|
tree
2010-08-12
R
ossen Apostolov
Me
r
ge branch
'
rel
e
ase-4-5-
p
atches' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
R
o
ssen Aposto
l
ov
W
a
rnings ab
o
ut using b
r
oken MPI implementatio
n
s
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen Apostolov
Updated the CMake s
c
ript
s
f
or find
i
ng CUDA, L
i
bXml2
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apostolov
Fixed broken linki
n
g with si
n
gl
e
pr
e
cision
f
f
t
w3
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apostolov
Ad
d
ed a new file INST
A
LL
.
cmake with installa
t
i
on i
n
structio
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen
A
postolo
v
Merge branch 'release-4-5-patch
e
s' of git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apost
o
lov
CMake builds now ins
t
a
ll GM
X
RC* files
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apostolov
F
i
x
for CMake builds so that they don
'
t
fai
l
e
ven when
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Rossen Apostolov
Bum
p
ed ver
s
i
o
n to
4
.
5-beta
3
commit
|
commitdiff
|
tree
2010-08-10
R
o
ssen Apostolov
Fix
e
d a typo
i
n
sr
c
/tool
s
/CMakeList
s
.
tx
t
.
commit
|
commitdiff
|
tree
2010-08-10
Rossen A
p
ostolov
Add
e
d m
i
ssin
g
NULL in chainsep enum in pdb2gmx
.
commit
|
commitdiff
|
tree
2010-08-04
Rossen Apostolov
F
i
x
s
h
are/html
/
on
l
ine/mdp_opt
.
html
.
commit
|
commitdiff
|
tree
2010-08-04
Rossen A
p
o
stolov
F
i
xed configure
.
ac typo regrad
i
ng
q
mmm-o
r
ca
.
commit
|
commitdiff
|
tree
2010-08-02
Rossen Apostol
o
v
New
beta release
.
commit
|
commitdiff
|
tree
2010-07-29
Ross
e
n Aposto
l
ov
Adde
d
*
.
pc
.
cmakein fil
e
s for distr
i
bu
t
ion
commit
|
commitdiff
|
tree
2010-07-29
Ros
s
en Apostolov
Removed
O
penMM
i
nterface from autoconf, use CMake instead
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Ap
o
stol
o
v
Fixed a typo in p
r
evious Makefile
.
am commit
commit
|
commitdiff
|
tree
2010-07-29
Ros
s
en Apo
s
tol
o
v
Added f
o
r dist
r
ibution som
e
extra files n
e
eded b
y
CMake
.
commit
|
commitdiff
|
tree
2010-07-29
Ross
e
n
Apostolov
M
e
rge b
r
anch 'master' of git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2010-07-29
Rossen
A
postolov
F
i
xed typos i
n
previous commit
.
commit
|
commitdiff
|
tree
2010-07-29
R
o
s
sen Apostolov
A
dded
m
issi
n
g ass
e
mbly f
i
l
e
s
in nonbon
d
ed/nb_kernel
_
x86_64
_
s
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Ross
e
n A
p
osto
l
o
v
More make distcheck fixes
.
commit
|
commitdiff
|
tree
2010-07-26
Rossen Apostol
o
v
make
distcheck fixes
commit
|
commitdiff
|
tree
2010-07-23
Ross
e
n
Apostol
o
v
Adju
s
t
ewald_rtol when
p
assing it to
O
p
enMM
.
commit
|
commitdiff
|
tree
2010-07-21
Rossen Aposto
l
ov
ewal
d
_rtol adjus
t
ment for
OpenM
M
.
commit
|
commitdiff
|
tree
2010-07-20
Rosse
n
A
postolov
Added S
H
A
R
ED_VERSI
O
N_I
N
FO
to libgmxpreprocess
.
commit
|
commitdiff
|
tree
2010-07-20
Ros
s
en Apostol
o
v
Moved the X1
1
autom
a
ke d
e
pende
n
cy fla
g
insi
d
e ngmx
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apos
t
o
lov
Dis
a
bled a
d
justmen
t
of ewald_rto
l
f
or OpenMM
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apos
t
olov
B
y
default GM
X
_
ACCELERAT
I
O
N
is now "au
t
o"
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolo
v
Added support for OpenMM-2
.
0, and CUDA-3
.
1 is now
r
equired
.
commit
|
commitdiff
|
tree
2010-07-02
Rossen Apostolov
Disable by default ia
6
4
a
s
s
embly loops
.
Those will
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
R
ossen Apostolov
M
e
rge b
r
anch 'master
'
of
g
it
.
gromacs
.
or
g
:
gromacs
commit
|
commitdiff
|
tree
2010-07-02
Rossen Apostolov
Disable Al
l
v
sAll kern
e
l
s
fo
r
very
small sy
s
t
ems (<
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Rossen Apost
o
lo
v
Ini
t
ial CTest s
u
pport
commit
|
commitdiff
|
tree
2010-06-23
Rossen Apos
t
olov
In
c
reased SHARED_VERSION
_
INFO to 6:0:0 (closing bug
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Ro
s
sen Apostolov
Small cleanup of the openmm sec
t
ion in mdrun
.
c
commit
|
commitdiff
|
tree
2010-06-16
Rossen
A
postolov
M
e
r
ge branch 'master
'
of git
.
gro
m
acs
.
org:groma
c
s
commit
|
commitdiff
|
tree
2010-06-16
Rossen Apostolov
Fixed the command line options for GPU
b
i
na
r
ies
.
commit
|
commitdiff
|
tree
2010-06-08
R
o
sse
n
Apost
o
lov
Merge branch 'master'
o
f
git
.
gromacs
.
org:gr
o
m
a
cs
commit
|
commitdiff
|
tree
2010-06-08
Rossen
A
po
s
tolov
Added
missing
C
-termin
a
l oxyge
n
s OC1 and OC2 to
t
he
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Rossen
Apostolov
Issue a w
a
rnin
g
abou
t
using
h
ard
c
oded OBC scale factors
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Rossen Apostolov
OpenM
M
i
n
terf
a
c
e
: issue
a w
a
rnin
g
when the specified
.
.
.
commit
|
commitdiff
|
tree
2010-05-14
R
ossen Apostolov
The re
l
ative error
for c
a
lculati
o
n of E
w
ald and PME
.
.
.
commit
|
commitdiff
|
tree
2010-05-12
Rossen
Apostolo
v
Me
r
ge b
r
anc
h
'master' of git
.
grom
a
c
s
.
org
:
g
r
omacs
commit
|
commitdiff
|
tree
2010-05-12
Ross
e
n Apo
s
t
olov
Fix
f
o
r
Ur
e
y-Bradley potential in OpenMM
commit
|
commitdiff
|
tree
2010-05-11
R
o
ssen Apostolov
Add
e
d s
u
pp
o
rt for Urey-Bradley
p
o
tentials to the openmm
.
.
.
commit
|
commitdiff
|
tree
2010-05-04
R
o
ssen Apostolov
F
i
xed im
p
roper
e
rr
o
r message in op
e
nmm_
w
rappe
r
.
commit
|
commitdiff
|
tree
2010-04-01
Rossen A
p
o
s
to
l
ov
Minor fixes of typos
.
commit
|
commitdiff
|
tree
2010-03-31
Rossen Apostolov
Fixed a
gmx_warn
i
ng cras
h
in openmm_wrapper
.
cpp
commit
|
commitdiff
|
tree
2010-03-31
R
o
ssen Apostolov
Fixed src/contrib/options
.
c
t
o
use the
new parse
_
common_args
.
.
.
commit
|
commitdiff
|
tree
2010-03-27
Rossen
Apostolov
OpenMM: "md" option is now ac
c
e
p
t
e
d
.
commit
|
commitdiff
|
tree
2010-03-24
R
ossen Apostolov
Allowing also CUDA
v
ersions later than 2
.
3
.
commit
|
commitdiff
|
tree
2010-03-24
Rossen Apostolov
Signal handlin
g
is
n
ow enabled for the openmm platform
.
commit
|
commitdiff
|
tree
2010-03-17
Rossen
A
post
o
lov
openmm: some
cleanup in md_openmm
.
c
a
n
d mdrun
.
c
commit
|
commitdiff
|
tree
2010-03-12
R
o
s
sen Apostolov
E
nabl
e
d checkpoints in Open
M
M
.
commit
|
commitdiff
|
tree
2010-03-12
Rossen
Apostolov
Automatically disa
b
le threads for OpenM
M
b
uilds
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apost
o
lov
Various fixes
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
Small
fixes in mdrun desc
.
;
e
n
a
ble
per
i
o
d
ic molecules
commit
|
commitdiff
|
tree
2010-03-11
Rossen
A
postol
o
v
Enalbed -maxh option
f
or
u
sage with Op
e
nMM binaries
commit
|
commitdiff
|
tree
2010-03-11
Ross
e
n Apostolov
C
l
e
ane
d
up do_md_openmm
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen A
p
ostolo
v
Reworked the i
n
te
g
rator and
t
hermostat
options
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apo
s
tolov
Fi
x
ed the
wrong output tim
e
frames
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostol
o
v
do_md_o
p
ennm
m
.
h
(
aka patched) now works but the time
.
.
.
commit
|
commitdiff
|
tree
2010-03-11
Ros
s
en Apostol
o
v
Initial porting,
do_md_openmm_nopatc
h
.
h is us
e
d
.
commit
|
commitdiff
|
tree
2009-10-02
Rossen
A
p
ostolov
U
sers are
n
ow refer
e
d to the new website in case of
.
.
.
commit
|
commitdiff
|
tree
2009-08-17
R
oss
e
n
A
postolov
Fixed incorrect scaling
o
f forces i
n
recip
r
ocal space
.
.
.
commit
|
commitdiff
|
tree