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Replace scoped_cptr with unique_cptr
2015-09-25
Ros
s
en A
p
o
sto
l
ov
Converted math to C++
.
commit
|
commitdiff
|
tree
2015-09-18
Ros
s
en Aposto
l
o
v
C
o
nverted membed
.
c to C
+
+
commit
|
commitdiff
|
tree
2015-09-12
R
ossen Apostolov
Converted pbcu
t
il
s
to C
+
+
commit
|
commitdiff
|
tree
2015-09-09
Rossen Apostolov
Co
n
verted
topology to C++
.
commit
|
commitdiff
|
tree
2015-09-07
R
os
s
e
n
A
p
ostolov
Converted i
m
d module to C++
.
commit
|
commitdiff
|
tree
2015-09-04
Rossen Apostolov
Con
v
erted
e
ssen
t
ialdynam
i
cs module to C+
+
.
commit
|
commitdiff
|
tree
2015-09-04
Rossen
A
postolov
Fi
x
ed
a typo
i
n OpenCL cm
a
ke s
y
ste
m
commit
|
commitdiff
|
tree
2015-07-24
Rossen Apostolov
C
onverted corr
e
lationfuntcions to C++
.
commit
|
commitdiff
|
tree
2015-06-15
Rossen Apostolov
Building
o
wn fftw
now uses vers
i
on 3
.
3
.
4
commit
|
commitdiff
|
tree
2015-06-02
R
ossen Apostolov
Convert
e
d r
a
ndom
module to C++
.
commit
|
commitdiff
|
tree
2015-05-27
R
ossen
A
postol
o
v
Converted pul
l
ing code to C
+
+
.
commit
|
commitdiff
|
tree
2015-05-12
R
ossen Apostolov
Added a note
a
bout sc-co
u
l being auto turned on
.
commit
|
commitdiff
|
tree
2014-09-26
Ros
s
en A
p
o
stolov
Conv
e
rt
e
d s
w
ap module t
o
C++
.
commit
|
commitdiff
|
tree
2014-09-09
Rossen
A
pos
t
olov
Converted g
r
ou
p
coor
d
t
o
C++
.
commit
|
commitdiff
|
tree
2014-09-09
Ross
e
n
A
p
ost
o
l
ov
C
o
nverted fft fi
l
es to C++
.
commit
|
commitdiff
|
tree
2014-06-29
R
ossen Apostolov
Us
e
co
s
istent style when referring to force fields
.
commit
|
commitdiff
|
tree
2014-06-27
Ros
s
e
n
Apostolov
Ch
a
n
g
ed linking order to m
a
ke Extrae work
.
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apo
s
to
l
ov
Added infor
m
ation ab
o
ut dihedral r
e
straints
.
commit
|
commitdiff
|
tree
2014-06-27
Rossen
A
postolov
Remove install_manifes
t
.
txt during
mak
e
c
lean
.
commit
|
commitdiff
|
tree
2014-06-24
R
o
ss
e
n Apostolov
E
x
t
end vers
i
o
n checking/warnings for checkpoint
c
ont
i
nu
a
tion
commit
|
commitdiff
|
tree
2014-06-23
Rossen Apostolo
v
Adde
d
tip5p
t
o the lis
t
of watermodel
s
in som
e
FF
.
commit
|
commitdiff
|
tree
2014-06-22
Rosse
n
A
p
o
stolov
Mo
r
e
c
lea
r
message fo
r
undef
i
ned
p
u
llgroups
.
commit
|
commitdiff
|
tree
2014-06-20
Rossen A
p
o
s
tolov
Fixed typo in
o
plsa
a
ASPH cha
r
g
es
.
commit
|
commitdiff
|
tree
2014-06-20
R
o
ssen Apostolov
Removed unus
e
d pa
r
ameters
a
n
d
c
l
eanup
of input
r
ec
.
commit
|
commitdiff
|
tree
2014-06-19
R
o
ssen Apostol
o
v
Small typos in surf
a
c
e
tension description
.
commit
|
commitdiff
|
tree
2014-06-18
Rossen
A
postolov
Add
e
d refe
r
e
n
ce
t
o cmap in pdb2gm
x
.
commit
|
commitdiff
|
tree
2014-06-17
Rossen Apostolov
S
mall
c
ha
n
g
es in appendix A of
t
h
e manu
a
l
.
commit
|
commitdiff
|
tree
2014-06-14
R
o
ssen
Apos
t
olov
Added tip5pe water model
t
o
o
plsa
.
commit
|
commitdiff
|
tree
2014-06-12
Rossen
Apostolov
Clea
n
up environment variables
.
commit
|
commitdiff
|
tree
2014-06-11
Ros
s
e
n
A
postolov
Ma
p
ped HIS
1
to HSD in charmm27
.
commit
|
commitdiff
|
tree
2014-06-10
Ro
s
sen Apostolov
Pr
i
nt in highe
r
p
r
ecision repl_ex tim
e
step
.
commit
|
commitdiff
|
tree
2014-06-09
R
o
s
s
en Apostolo
v
Is
s
u
e
a warnin
g
for u
s
ing gmx_rms
-
p
r
ev with
large
.
.
.
commit
|
commitdiff
|
tree
2014-06-09
Rosse
n
A
postolov
I
nstall librari
e
s in corr
e
ct directories on multiarch
.
.
.
commit
|
commitdiff
|
tree
2014-06-09
Rosse
n
Aposto
l
ov
Fixed typo i
n
desc
r
iption of
c
o
nversion
f
actor
s
.
commit
|
commitdiff
|
tree
2014-06-04
Ros
s
en Apostolov
Updated C-/N-termin
a
l partial charges
in Amber03
.
ff
.
commit
|
commitdiff
|
tree
2014-05-24
R
ossen Apostolov
Simp
l
ified section
"Port
i
ng"
.
commit
|
commitdiff
|
tree
2014-05-24
R
oss
e
n
A
postolov
Allow
trjc
o
nv to keep some box dimensions unchanged
.
commit
|
commitdiff
|
tree
2014-05-22
Rossen
A
post
o
lo
v
Normal mo
d
es don't work currently wit
h
vir
t
ua
l
si
t
es
.
.
.
commit
|
commitdiff
|
tree
2014-05-20
Ros
s
e
n
Apostolov
A
dded a n
o
t
e a
b
out using direction-per
i
odi
c
p
u
lli
n
g
.
commit
|
commitdiff
|
tree
2014-05-20
Rossen Apostolov
Added a note
about unsuppor
t
ed V
e
rlet cuto
f
f
+ Buckingham
.
commit
|
commitdiff
|
tree
2014-03-31
Rossen
A
p
o
stolov
Ad
d
ed CMake supp
o
rt for Extrae
.
commit
|
commitdiff
|
tree
2014-03-17
Rossen
Apostolov
Cleane
d
up end
i
f
/else-s
i
n CMakeL
i
sts
.
tx
t
and *
.
cmake
.
.
.
commit
|
commitdiff
|
tree
2014-03-11
Rossen A
p
ostolov
R
em
o
ved
.
i
t
p files from top
l
evel
directory
.
commit
|
commitdiff
|
tree
2014-03-06
Ros
s
en
A
postolov
R
e
m
o
v
e
d the deprec
a
te
d
g
m
x
.
f
f and gmx2
.
ff
.
commit
|
commitdiff
|
tree
2014-02-23
Rossen Apostolov
Removed deprecated Encad FF
.
commit
|
commitdiff
|
tree
2014-02-20
Rossen Ap
o
stolov
Rename
f
fopen and ffclose to gmx_ff*
.
commit
|
commitdiff
|
tree
2014-01-30
Ros
s
en Apostol
o
v
Removed ions
.
itp from GMX/s
h
are
/
t
op
d
irector
y
.
commit
|
commitdiff
|
tree
2014-01-28
Rossen
Aposto
l
ov
Bump own
f
ftw
b
u
ild
to version 3
.
3
.
3
commit
|
commitdiff
|
tree
2014-01-21
Ross
e
n Apostolov
Fixed wron
g
messa
g
e
w
hen
b
uil
d
ing own
FFTW
.
commit
|
commitdiff
|
tree
2013-11-28
Rossen Apo
s
tolov
Updat
e
d to gm
o
c
k
-1
.
7
.
0
commit
|
commitdiff
|
tree
2011-11-25
Ross
e
n Aposto
l
o
v
Added s
u
pport
for submission
t
o cdas
h
servers
.
commit
|
commitdiff
|
tree
2011-09-27
Rosse
n
Apostolov
Merg
e
"
R
e
moved CMak
e
warning for
r
ecent Op
e
nMPI versions
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
Rossen Apostolov
Update
d
ve
r
sion: now 4
.
6
commit
|
commitdiff
|
tree
2011-09-20
Rossen Apostol
o
v
New release: 4
.
5
.
5
commit
|
commitdiff
|
tree
2011-09-19
Rossen Apostolo
v
Merge "Resolved g
e
r
r
it is
s
ue
h
ttps://ger
r
it
.
groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
Rossen Aposto
l
ov
Added support for
g
_
dos,
g
_hy
d
order and g_denso
r
der
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
Rossen Apostol
o
v
Fixed a bu
g
in egbOBC and double precission
.
commit
|
commitdiff
|
tree
2011-09-16
Rossen Apostolov
Me
r
ge "g_wh
a
m
:
fixed pullx
.
x
v
g rea
d
ing issue w
i
th pull_ge
o
me
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Rossen
Apostolov
Merge "Add
e
d war
n
ing line
.
" into releas
e
-4-5-patches
commit
|
commitdiff
|
tree
2011-09-13
R
o
s
sen Apos
t
olov
M
e
r
g
e "Fixes for CMake finding FORTRAN library names
.
.
.
commit
|
commitdiff
|
tree
2011-09-09
Ros
s
en Apos
t
olov
Add
e
d support f
o
r cu
s
tom
e
xternal BLAS/LAP
A
C
K
li
b
r
a
ries
.
commit
|
commitdiff
|
tree
2011-05-18
Ross
e
n Apostolov
F
ixed g_tcaf
citation
in html docs
commit
|
commitdiff
|
tree
2011-03-21
Rossen Apostolov
New maintenan
c
e release: 4
.
5
.
4
commit
|
commitdiff
|
tree
2011-03-21
R
o
ssen
Ap
o
stolov
Fixed more r
e
al/doub
l
e
i
ssu
e
s in gmx_density
commit
|
commitdiff
|
tree
2011-03-21
Rosse
n
Aposto
l
ov
Removed du
p
licate
d
EXT
R
A
_DI
S
T entry in src/tool
s
/
Makefiles
.
am
commit
|
commitdiff
|
tree
2011-03-21
Rossen
A
postolov
Added back
T
emplate
.
m
a
k
.
commit
|
commitdiff
|
tree
2011-03-21
Ros
s
en
Apostol
o
v
Remove
d
some templa
t
e files from installatio
n
.
commit
|
commitdiff
|
tree
2011-03-14
Ro
s
sen Apostolo
v
g_options
so
u
r
c
e files a
r
e n
o
w properly packaged
commit
|
commitdiff
|
tree
2010-12-16
Ro
s
s
e
n Apostolo
v
Anothe
r
t
e
st c
o
mmit
commit
|
commitdiff
|
tree
2010-12-15
Rossen Apostol
o
v
T
e
st commit
commit
|
commitdiff
|
tree
2010-11-09
Ros
s
en Apostolov
New maintana
n
ce
release: 4
.
5
.
3
commit
|
commitdiff
|
tree
2010-11-08
Ross
e
n Apost
o
l
o
v
Revertin
g
back GMX
_
DLOPEN to defa
u
l
t
O
N
commit
|
commitdiff
|
tree
2010-11-08
Rossen Apostolov
Disable G
M
X
_DLOPEN by default
.
commit
|
commitdiff
|
tree
2010-11-08
Rossen Apostolov
Added suppo
r
t for Alt
i
v
ec kernels on P
O
WERPC
.
commit
|
commitdiff
|
tree
2010-10-30
Ro
s
s
e
n Ap
o
stolov
Added
b
a
c
k the "-dev"
s
uffixe
s
to the versio
n
stri
n
gs
.
commit
|
commitdiff
|
tree
2010-10-30
Rossen A
p
os
t
olo
v
New bug
f
ix releas
e
: 4
.
5
.
2
commit
|
commitdiff
|
tree
2010-10-30
Rossen Apostolov
Fo
r
MPI build
s
, CMake will fir
s
t try to compile a sa
m
p
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-10-29
Rossen Apostolov
added g
_
kinetics to the CMake buil
d
script
s
commit
|
commitdiff
|
tree
2010-09-25
Rossen
A
postolov
Reve
r
t
ed chang
e
s to
md_openmm
.
c,
get rid
of
'
nan' in
.
.
.
commit
|
commitdiff
|
tree
2010-09-25
Rossen Apostolo
v
mdrun-
g
pu
n
o
w
doesn
'
t
output indivi
d
ual ene
r
gy
t
erm
.
.
.
commit
|
commitdiff
|
tree
2010-09-21
Rossen Apost
o
lov
Fixed missing installa
t
io
n
of
t
he
o
penm
m
_api_wrapper
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
Rosse
n
Apostolo
v
Adde
d
do_multiprot i
n
s
r
c
/
co
n
t
r
ib
,
thanks to Ran
F
r
iedman
commit
|
commitdiff
|
tree
2010-09-13
Rossen Apo
s
tolov
Add
e
d d
e
p
endencies for ope
n
mm_
a
pi_wrapper
commit
|
commitdiff
|
tree
2010-09-13
Ros
s
en A
p
ostolov
A
d
d
ed library
dependency for gmx_gpu_utils
commit
|
commitdiff
|
tree
2010-09-07
Rossen
A
postolov
Merg
e
br
a
nch 'release
-
4-5-patches'
commit
|
commitdiff
|
tree
2010-09-06
Rossen A
p
osto
l
ov
Added a no
t
e tha
t
ru
n
n
i
ng in double precision is
slow
e
r
.
commit
|
commitdiff
|
tree
2010-09-06
Rossen
A
postolov
A lot of CMa
k
e options a
r
e now m
a
rke
d
a
s
advan
c
e
d since
.
.
.
commit
|
commitdiff
|
tree
2010-09-02
Rossen Apostolov
A
n
o
ther missi
n
g CMake file
.
commit
|
commitdiff
|
tree
2010-09-02
Rosse
n
Apostolov
Merge
b
r
a
nch 'release-4-5-patch
e
s
'
commit
|
commitdiff
|
tree
2010-09-02
Rossen Apostolov
Updated
the ve
r
sion
numbers to
4
.
5
.
1
.
commit
|
commitdiff
|
tree
2010-09-02
Ro
s
sen A
p
ostolov
Added for distribution missing C
M
ake spe
c
i
f
ic fi
l
es
.
commit
|
commitdiff
|
tree
2010-09-01
Rossen
Apostolov
New release: 4
.
5
(
f
i
nal)
.
Ya
y
!
!
!
commit
|
commitdiff
|
tree
2010-09-01
Ros
s
en Apostolov
A
dded g_rm
s
dist and g_rotmat
to
t
he CMake bui
l
d system
commit
|
commitdiff
|
tree
2010-09-01
Rossen A
p
ostolov
S
m
al
l
update
of the GPU related documentation
.
commit
|
commitdiff
|
tree
2010-09-01
Rossen
Apostolov
Small
u
pdate o
f
th
e
GPU related
documentati
o
n
.
commit
|
commitdiff
|
tree
2010-09-01
Ro
s
sen Apostolov
M
erge branch 'release-4
-
5
-patches' of
g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Rossen Ap
o
stolov
Merge b
r
a
nc
h
'
r
elease-4-5-patches' o
f
git
.
groma
c
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Rossen Apostolov
Merge bran
c
h
'rele
a
se-4-5-pa
t
ches' o
f
git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Rosse
n
Apo
s
t
olov
OpenMM no
w
accep
t
s
cut-off method,
s
ince
it's ne
e
ded
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Rossen Apostolov
N
e
w
release 4
.
5-beta
4
commit
|
commitdiff
|
tree
next