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OpenMM now accepts cut-off method, since it's needed for implicit solvent calculations.
2010-08-31
R
o
ssen Apostolov
OpenMM no
w
acc
e
pts cut-off method, since it's ne
e
ded
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Rossen Apostolov
New re
l
e
a
se 4
.
5
-
beta4
commit
|
commitdiff
|
tree
2010-08-26
Rosse
n
Aposto
l
ov
Mo
d
ifi
e
d the
O
penMM w
r
apper inter
f
ace to
s
upport t
h
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
R
o
s
sen Apostolov
Adde
d
the g_pme_error too
l
f
r
om Florian
Dommert
.
Thanks!
commit
|
commitdiff
|
tree
2010-08-26
R
ossen Apos
t
olov
Fix
e
d
hardcode
d
OpenMM library name
.
commit
|
commitdiff
|
tree
2010-08-26
Rossen Aposto
l
ov
R
em
o
ved the
u
nn
e
c
e
s
sary hacks from some boolean statements
.
commit
|
commitdiff
|
tree
2010-08-25
Rossen Apo
s
tolov
Red
e
f
ine t
h
e d
e
fault
b
oolea
n
type to g
m
x_b
o
o
l
.
commit
|
commitdiff
|
tree
2010-08-23
Rossen Apostolov
Merge branch 'rel
e
ase-4
-
5-pat
c
hes' of
git
.
gromac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-23
Rossen Apostolov
F
i
xed a ty
p
o about
n
on-existing
m
acro
in
O
penMM
commit
|
commitdiff
|
tree
2010-08-19
Rossen Aposto
l
o
v
Enable
the Reference plat
f
orm for OpenMM
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen Apost
o
l
ov
Merge branc
h
'releas
e
-4-5-patches' of
git
.
g
roma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Rosse
n
Apostolo
v
F
ixed
the
executio
n
orde
r
in
Open
M
M
s
o that the g
e
nerated
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Rossen A
p
o
stolov
Pres
e
rve th
e
.
pl
e
xtentions to
s
cr
i
pts
.
commit
|
commitdiff
|
tree
2010-08-16
Ross
e
n Apo
s
tolo
v
Removed
the nb_
k
ernel4xx_in
t
el
_
s
ynta
x
.
c entries from
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Rossen A
p
ostolov
Add
e
d support fo
r
improper dihedra
l
s needed for CHARMM
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Ro
s
sen
A
postolov
OpenMM: added support for AmberFF pr
o
per/improper torsion
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen Apostol
o
v
Fixed
a r
e
vert
e
d
versi
o
n strin
g
in
configur
e
.
ac
commit
|
commitdiff
|
tree
2010-08-12
Ross
e
n Ap
o
stolov
M
erg
e
b
r
an
c
h 'rele
a
se-4-5-patche
s
'
o
f git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-12
Rossen A
p
ostolov
W
a
rnin
g
s
a
bout
using broken
MP
I
imp
l
ementations
.
commit
|
commitdiff
|
tree
2010-08-12
R
o
ssen Apostolov
Updated the CMake
scripts
for finding CU
D
A, LibXml2
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
R
o
ssen Apostolov
Fix
e
d broken
l
i
n
king w
i
th si
n
gle pr
e
cis
i
on fftw
3
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apost
o
lo
v
Adde
d
a new fi
l
e INSTAL
L
.
cmake with installation instructio
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
R
o
ssen Ap
o
stolov
Merge
b
ranch
'
release-4-5-patches
'
of git
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
Rossen Apost
o
lov
CMake buil
d
s now install GMXRC*
f
iles
.
commit
|
commitdiff
|
tree
2010-08-11
Rosse
n
Apostolov
Fix for CMake builds
s
o that they don't fa
i
l eve
n
when
.
.
.
commit
|
commitdiff
|
tree
2010-08-10
Rosse
n
Apostolov
Bumpe
d
version to 4
.
5
-
b
eta3
commit
|
commitdiff
|
tree
2010-08-10
Rossen A
p
ostolov
Fixed a typ
o
in src/tool
s
/CMakeLis
t
s
.
txt
.
commit
|
commitdiff
|
tree
2010-08-10
Rossen Apos
t
o
l
ov
A
d
d
ed
m
issing N
U
L
L in chainsep e
n
um in pdb2gmx
.
commit
|
commitdiff
|
tree
2010-08-04
Rossen Apostolov
Fix share/html/online/mdp_opt
.
html
.
commit
|
commitdiff
|
tree
2010-08-04
Rossen Ap
o
s
t
olov
Fixe
d
c
o
nfigure
.
ac typo regrading
q
mmm-
o
rca
.
commit
|
commitdiff
|
tree
2010-08-02
Rosse
n
Aposto
l
o
v
N
ew b
e
ta release
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen A
p
ostolov
A
d
ded
*
.
p
c
.
c
makei
n
files for distri
b
ut
i
on
commit
|
commitdiff
|
tree
2010-07-29
Ros
s
en
Apost
o
lov
Removed Ope
n
MM inte
r
face from autoconf, u
s
e CMa
k
e instead
.
.
.
commit
|
commitdiff
|
tree
2010-07-29
Ross
e
n
A
p
ostolov
Fixed a typo in p
r
evious Makefile
.
am
comm
i
t
commit
|
commitdiff
|
tree
2010-07-29
Rossen
Apostolov
A
d
ded fo
r
d
i
stributi
o
n som
e
extra file
s
needed by CMake
.
commit
|
commitdiff
|
tree
2010-07-29
Rossen Apo
s
tolov
Merge branch
'
master' of git
.
gr
o
mac
s
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-07-29
Rossen Ap
o
st
o
lo
v
Fixed t
y
p
os in previous commit
.
commit
|
commitdiff
|
tree
2010-07-29
R
os
s
en Apostolov
Adde
d
mis
s
ing assem
b
ly files in nonbonded/nb
_
kern
e
l_x86_64_s
.
.
.
commit
|
commitdiff
|
tree
2010-07-26
Rossen Apostolov
More
m
ake distcheck
f
ixe
s
.
commit
|
commitdiff
|
tree
2010-07-26
Rossen
A
p
ostolov
make d
i
s
t
check fixe
s
commit
|
commitdiff
|
tree
2010-07-23
Ro
s
s
e
n Apostolov
Adju
s
t
ewald_rtol when passi
n
g it
to
OpenMM
.
commit
|
commitdiff
|
tree
2010-07-21
Rossen Apostolo
v
ewald_rto
l
adjus
t
ment for OpenMM
.
commit
|
commitdiff
|
tree
2010-07-20
Rosse
n
Apostolov
Added SHARED_VERSION_INFO to li
b
gmxprep
r
ocess
.
commit
|
commitdiff
|
tree
2010-07-20
Ro
s
se
n
Apost
o
l
ov
Moved the X11 automake d
e
pend
e
ncy flag
insid
e
ngmx
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolo
v
Di
s
abl
e
d adj
u
s
tm
e
nt of
ewald
_
rtol
f
o
r
OpenMM
.
commit
|
commitdiff
|
tree
2010-07-20
Rossen Apostolov
By default GMX_
A
C
C
ELERATI
O
N is now "a
u
to"
.
commit
|
commitdiff
|
tree
2010-07-20
Ros
s
en Apo
s
tol
o
v
Add
e
d
support for
O
penMM-2
.
0
,
and CUDA-3
.
1 is now
r
equired
.
commit
|
commitdiff
|
tree
2010-07-02
R
o
ssen
A
postolov
D
i
s
able by default ia6
4
a
s
semb
l
y
loops
.
T
h
ose will
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Rosse
n
A
p
ostol
o
v
Merge branch
'
mas
t
e
r
' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-07-02
Rossen Apo
s
to
l
ov
Disable
A
llvsA
l
l kernels for
very small sys
t
ems (<
.
.
.
commit
|
commitdiff
|
tree
2010-06-24
Rossen A
p
ostolov
Initial CTest support
commit
|
commitdiff
|
tree
2010-06-23
Rossen Apostolov
Increased SHA
R
E
D_
V
ERSI
O
N_INFO to 6:0:0 (closi
n
g bug
.
.
.
commit
|
commitdiff
|
tree
2010-06-16
Rossen A
p
osto
l
ov
Small
c
leanup of the open
m
m
secti
o
n in mdrun
.
c
commit
|
commitdiff
|
tree
2010-06-16
R
os
s
e
n Apostolov
M
erge branc
h
'maste
r
' of g
i
t
.
gromacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2010-06-16
R
osse
n
Aposto
l
ov
Fi
x
ed the
comma
n
d line options for GPU
b
inarie
s
.
commit
|
commitdiff
|
tree
2010-06-08
R
o
s
s
en Apostolov
Mer
g
e br
a
nch '
m
a
ster' of
g
i
t
.
gr
o
macs
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-06-08
Rosse
n
Apost
o
lov
Added missing
C
-termin
a
l oxygen
s
OC1 and OC2 t
o
th
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Rossen Apostolov
Issue
a
warning about using hardcoded OBC
s
cale factors
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
R
o
sse
n
Apostolov
OpenMM interface: issue a war
n
in
g
when the
s
pecified
.
.
.
commit
|
commitdiff
|
tree
2010-05-14
Ross
e
n Apostolov
The relative error f
o
r calc
u
l
ation of
Ewal
d
and
P
ME
.
.
.
commit
|
commitdiff
|
tree
2010-05-12
R
ossen Apostolo
v
Merg
e
bra
n
ch 'm
a
ster'
o
f
g
i
t
.
gr
o
mac
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-05-12
R
oss
e
n Apost
o
lov
Fix for Urey
-
B
r
a
d
ley po
t
e
ntial in Ope
n
MM
commit
|
commitdiff
|
tree
2010-05-11
R
osse
n
Ap
o
stolov
Added support
fo
r
Urey-
B
radley
potentials t
o
th
e
openmm
.
.
.
commit
|
commitdiff
|
tree
2010-05-04
Rossen Ap
o
stolov
Fixed
improper err
o
r message in openmm_wra
p
per
.
commit
|
commitdiff
|
tree
2010-04-01
Rossen Apostolov
Minor fixes
o
f typos
.
commit
|
commitdiff
|
tree
2010-03-31
R
ossen Apostolov
Fixed
a gmx_warnin
g
cr
a
sh i
n
ope
n
mm_wrapper
.
cpp
commit
|
commitdiff
|
tree
2010-03-31
Rossen Apost
o
lov
Fixed src/con
t
rib/op
t
i
ons
.
c to use
the new parse_common_args
.
.
.
commit
|
commitdiff
|
tree
2010-03-27
Rossen Apostolov
O
p
enMM: "md" option is now acc
e
p
t
e
d
.
commit
|
commitdiff
|
tree
2010-03-24
Rossen Apos
t
olov
A
l
lowing als
o
C
UDA
versions late
r
than 2
.
3
.
commit
|
commitdiff
|
tree
2010-03-24
R
ossen Apostolov
Signal handling
is now enabled for t
h
e
o
p
enmm platf
o
rm
.
commit
|
commitdiff
|
tree
2010-03-17
Rossen Apostolov
o
p
en
m
m: som
e
c
l
e
anu
p
in md_open
m
m
.
c and mdrun
.
c
commit
|
commitdiff
|
tree
2010-03-12
Rossen Apost
o
lov
Enabl
e
d checkpoints in OpenMM
.
commit
|
commitdiff
|
tree
2010-03-12
Ros
s
en Apostolov
Automa
t
ically disable th
r
eads
for OpenMM bu
i
lds
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen
A
post
o
lov
Var
i
ous f
i
xes
.
commit
|
commitdiff
|
tree
2010-03-11
Rosse
n
Apostolov
Small fixes in mdrun desc
.
; enable perio
d
ic molecules
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
Ena
l
bed
-maxh
o
ption fo
r
us
a
g
e
with Ope
n
M
M
bin
a
ries
commit
|
commitdiff
|
tree
2010-03-11
Ross
e
n Apos
t
o
lov
Cleaned up do_md_openmm
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolo
v
Reworked the int
e
gra
t
or an
d
the
r
mostat
o
pt
i
ons
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
Fix
e
d
t
he wrong output time frames
commit
|
commitdiff
|
tree
2010-03-11
Rossen Apostolov
d
o
_
m
d
_
op
e
nnmm
.
h
(
aka patched)
n
ow works but the time
.
.
.
commit
|
commitdiff
|
tree
2010-03-11
Rossen
A
p
o
s
to
l
ov
Initial porting, do
_
md_openmm_
n
opatch
.
h is used
.
commit
|
commitdiff
|
tree
2009-10-02
Ross
e
n Apostolov
Users are now ref
e
red to the new website in ca
s
e of
.
.
.
commit
|
commitdiff
|
tree
2009-08-17
Rossen Apost
o
l
ov
F
i
xed incorr
e
ct
scaling
o
f f
o
r
c
e
s
in reci
p
r
ocal space
.
.
.
commit
|
commitdiff
|
tree