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Fixes newly introduced bug in make_ndx.
2015-09-25
R
ossen Apos
t
olov
Co
n
ver
t
ed math to C++
.
commit
|
commitdiff
|
tree
2015-09-18
Ros
s
en Apost
o
lov
Con
v
erted membed
.
c
to C++
commit
|
commitdiff
|
tree
2015-09-12
Rossen Apostolo
v
Converted
pbcutils to
C++
commit
|
commitdiff
|
tree
2015-09-09
Rossen Apostolov
Converted topology to C++
.
commit
|
commitdiff
|
tree
2015-09-07
Rossen Aposto
l
o
v
Converted imd
mod
u
le
to C++
.
commit
|
commitdiff
|
tree
2015-09-04
Rosse
n
Apostolov
C
o
nverted essen
t
ialdy
n
amics mod
u
l
e
to C++
.
commit
|
commitdiff
|
tree
2015-09-04
Rosse
n
Apostolov
Fi
x
e
d
a
typo in OpenCL cma
k
e s
y
stem
commit
|
commitdiff
|
tree
2015-07-24
R
o
ssen Apostolo
v
C
on
v
er
t
e
d correlati
o
nf
u
n
tc
i
o
n
s t
o
C
+
+
.
commit
|
commitdiff
|
tree
2015-06-15
R
o
s
sen Apost
o
lov
Build
i
n
g
ow
n
fftw now
uses version 3
.
3
.
4
commit
|
commitdiff
|
tree
2015-06-02
R
o
ssen Apostolov
C
o
nverted random module to C++
.
commit
|
commitdiff
|
tree
2015-05-27
Rossen Apo
s
tolov
Conv
e
rted pulling code
t
o C++
.
commit
|
commitdiff
|
tree
2015-05-12
Rossen Apostolov
Adde
d
a note about sc-coul being auto tu
r
ned on
.
commit
|
commitdiff
|
tree
2014-09-26
Rossen Apostolov
Converted swap mod
u
le to C++
.
commit
|
commitdiff
|
tree
2014-09-09
Ro
s
sen A
p
ostol
o
v
Con
v
e
r
te
d
gro
u
pcoo
r
d to C++
.
commit
|
commitdiff
|
tree
2014-09-09
R
o
s
s
e
n Apo
s
t
o
lov
Co
n
verted
f
f
t
files
to
C
++
.
commit
|
commitdiff
|
tree
2014-06-29
R
ossen Apostolov
Use cosistent style when referri
n
g to f
o
rce fields
.
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apostolov
Changed link
i
ng o
r
der to make Ex
t
rae
w
o
r
k
.
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apo
s
to
l
o
v
Adde
d
information abo
u
t dihedral r
e
straints
.
commit
|
commitdiff
|
tree
2014-06-27
R
o
ssen Ap
o
s
t
ol
o
v
Remov
e
i
n
st
a
ll_man
i
fest
.
txt during make cle
a
n
.
commit
|
commitdiff
|
tree
2014-06-24
Rossen Ap
o
s
t
o
lov
Extend version
c
hecking/war
n
ings for
c
heckpoint cont
i
nuation
commit
|
commitdiff
|
tree
2014-06-23
Rossen Apostolov
Ad
d
ed tip5p to t
h
e list
o
f watermo
d
e
ls
i
n
some
FF
.
commit
|
commitdiff
|
tree
2014-06-22
Rossen Apostolo
v
More clear me
s
sage for u
n
defined pul
l
g
r
o
ups
.
commit
|
commitdiff
|
tree
2014-06-20
Ro
s
sen Apostolov
Fixed typo in
oplsaa ASPH charges
.
commit
|
commitdiff
|
tree
2014-06-20
R
o
ssen
A
post
o
lov
Remov
e
d unused
param
e
ters
a
nd clean
u
p of inputrec
.
commit
|
commitdiff
|
tree
2014-06-19
Rosse
n
Apostolov
Small typos
in surface
tension
descr
i
ption
.
commit
|
commitdiff
|
tree
2014-06-18
R
o
ssen
Apostolov
Add
e
d re
f
erence t
o
cmap
i
n
p
db2gm
x
.
commit
|
commitdiff
|
tree
2014-06-17
Rossen
A
postolov
Small changes in appendix
A
of the manual
.
commit
|
commitdiff
|
tree
2014-06-14
Rossen Apostolov
Added tip5pe water m
o
del to op
l
sa
.
commit
|
commitdiff
|
tree
2014-06-12
Ros
s
en
A
po
s
t
olov
Clea
n
up environment
v
aria
b
les
.
commit
|
commitdiff
|
tree
2014-06-11
Rossen A
p
ost
o
lov
M
apped
H
IS1 t
o
H
SD i
n
charmm2
7
.
commit
|
commitdiff
|
tree
2014-06-10
R
oss
e
n Apostol
o
v
Prin
t
in high
e
r prec
i
sion r
e
pl_ex timeste
p
.
commit
|
commitdiff
|
tree
2014-06-09
Rossen Apostol
o
v
I
s
s
u
e a warning for
u
sing
gmx_rms -prev with large
.
.
.
commit
|
commitdiff
|
tree
2014-06-09
Ros
s
en Apostolov
Ins
t
a
ll libraries in corr
e
ct dire
c
tories on multiarch
.
.
.
commit
|
commitdiff
|
tree
2014-06-09
R
ossen Apostolov
F
i
xed typo in
d
escription of conv
e
rs
i
on factors
.
commit
|
commitdiff
|
tree
2014-06-04
Ro
s
sen
Apostolov
U
pdated C-
/
N-terminal partial char
g
es in Amber03
.
ff
.
commit
|
commitdiff
|
tree
2014-05-24
Rossen Ap
o
st
o
lov
Simplified section "P
o
rting"
.
commit
|
commitdiff
|
tree
2014-05-24
Rossen Ap
o
stolov
Allow trjconv
to kee
p
some box
d
imensions unch
a
nged
.
commit
|
commitdiff
|
tree
2014-05-22
Rossen Apostolov
N
o
r
mal modes don't wo
r
k currently with virtual site
s
.
.
.
commit
|
commitdiff
|
tree
2014-05-20
Rossen
A
p
o
stolov
Add
e
d a note
a
bout using
d
irect
i
on-periodic pulling
.
commit
|
commitdiff
|
tree
2014-05-20
Rossen
Apostolo
v
Added a note ab
o
ut unsupport
e
d Verlet cutoff
+ Bucki
n
g
ham
.
commit
|
commitdiff
|
tree
2014-03-31
Rossen
Apostolov
Added CMake support
f
or
Extrae
.
commit
|
commitdiff
|
tree
2014-03-17
Rosse
n
Aposto
l
ov
Clea
n
ed up endif/
e
lse-s
i
n
C
Mak
e
L
i
sts
.
txt and *
.
cmake
.
.
.
commit
|
commitdiff
|
tree
2014-03-11
Rossen Apostolov
Removed
.
it
p
fil
e
s f
r
o
m
top le
v
el directory
.
commit
|
commitdiff
|
tree
2014-03-06
Rossen
A
post
o
lov
R
e
mo
v
ed the
d
eprecated gmx
.
f
f
and
g
mx2
.
ff
.
commit
|
commitdiff
|
tree
2014-02-23
R
ossen
A
po
s
tolov
Remove
d
d
epr
e
cated
E
ncad FF
.
commit
|
commitdiff
|
tree
2014-02-20
Ross
e
n Apos
t
olo
v
Rename
f
fop
e
n and
f
f
close to gmx_ff*
.
commit
|
commitdiff
|
tree
2014-01-30
R
ossen Ap
o
stolov
Remov
e
d
ions
.
itp
f
rom GMX
/
sh
a
re
/
top direct
o
ry
.
commit
|
commitdiff
|
tree
2014-01-28
R
o
ssen Apost
o
lo
v
Bump own fftw buil
d
t
o
ve
r
si
o
n 3
.
3
.
3
commit
|
commitdiff
|
tree
2014-01-21
R
o
s
sen Aposto
l
ov
F
i
x
ed wron
g
message whe
n
b
uilding own FFTW
.
commit
|
commitdiff
|
tree
2013-11-28
Rossen Apostol
o
v
U
pdated to gm
o
c
k-1
.
7
.
0
commit
|
commitdiff
|
tree
2011-11-25
R
o
ssen
Apostolov
A
d
ded support for submission
t
o
c
d
a
sh
serv
e
rs
.
commit
|
commitdiff
|
tree
2011-09-27
Rossen
Apo
s
tolov
M
e
r
g
e "Removed CMake
w
ar
n
ing for recent O
p
enM
P
I ve
r
s
i
o
ns
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
Rossen Apostolov
Updated ve
r
sion: now 4
.
6
commit
|
commitdiff
|
tree
2011-09-20
Rossen
A
postolov
N
ew release: 4
.
5
.
5
commit
|
commitdiff
|
tree
2011-09-19
R
o
ssen
Apo
s
tolo
v
Merg
e
"Res
o
lved gerrit issue https
:
/
/gerrit
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
R
o
ssen
Apost
o
lov
Added support f
o
r g_dos,
g_h
y
dorde
r
a
nd g_de
n
sorder
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
R
o
ssen Ap
o
stolov
F
ixed a bug in
egbOBC and dou
b
le precission
.
commit
|
commitdiff
|
tree
2011-09-16
Ross
e
n Apostolov
Merge
"g_wham: fix
e
d p
u
llx
.
xvg readi
n
g issue with pull_g
e
ome
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Ross
e
n Aposto
l
o
v
Merge "Ad
d
ed warn
i
ng line
.
" into releas
e
-4-5-patches
commit
|
commitdiff
|
tree
2011-09-13
Rossen Apostolov
Merge "Fixes for CMake
f
in
d
ing F
O
R
T
R
AN library names
.
.
.
commit
|
commitdiff
|
tree
2011-09-09
Rossen A
p
ost
o
lov
Added supp
o
rt for custom ex
t
ernal BLA
S
/LAP
A
CK libraries
.
commit
|
commitdiff
|
tree
2011-05-18
R
o
sse
n
Apostolov
F
i
xed g_tcaf
c
i
tation in h
t
ml doc
s
commit
|
commitdiff
|
tree
2011-03-21
R
os
s
e
n Apos
t
olov
New maint
e
na
n
ce
r
elease: 4
.
5
.
4
commit
|
commitdiff
|
tree
2011-03-21
R
ossen Apostolov
Fixed more real/double issues in
g
mx_density
commit
|
commitdiff
|
tree
2011-03-21
Rosse
n
Apo
s
tolov
Removed
d
uplicated E
X
T
R
A
_DI
S
T
entry in src/tools/
M
a
kefiles
.
a
m
commit
|
commitdiff
|
tree
2011-03-21
Ross
e
n Apostolov
Ad
d
ed back T
e
mplat
e
.
mak
.
commit
|
commitdiff
|
tree
2011-03-21
R
o
s
s
en Apostolov
Removed some template fil
e
s from installation
.
commit
|
commitdiff
|
tree
2011-03-14
Rossen
A
post
o
lov
g_optio
n
s sourc
e
files are now properl
y
packaged
commit
|
commitdiff
|
tree
2010-12-16
R
o
s
sen Apo
s
tolov
Another tes
t
commit
commit
|
commitdiff
|
tree
2010-12-15
Rossen Apo
s
tolov
Test comm
i
t
commit
|
commitdiff
|
tree
2010-11-09
Rossen Apostol
o
v
Ne
w
maintana
n
c
e
r
e
leas
e
: 4
.
5
.
3
commit
|
commitdiff
|
tree
2010-11-08
Rosse
n
Apost
o
lov
Re
v
erting back GMX_
D
LOPEN
t
o default O
N
commit
|
commitdiff
|
tree
2010-11-08
Rossen Apostol
o
v
D
isa
b
le GMX_DLOPEN
b
y
d
efa
u
lt
.
commit
|
commitdiff
|
tree
2010-11-08
Ros
s
en Apost
o
lov
A
d
ded
support
f
or Alt
i
vec
k
ern
e
ls on POWERP
C
.
commit
|
commitdiff
|
tree
2010-10-30
Rossen Ap
o
stolov
Ad
d
ed ba
c
k th
e
"-dev"
s
uffixes to the version str
i
n
gs
.
commit
|
commitdiff
|
tree
2010-10-30
Rosse
n
Apostolov
N
ew
b
ugfix r
e
l
ease:
4
.
5
.
2
commit
|
commitdiff
|
tree
2010-10-30
Rossen Apostolov
For
M
PI build
s
, CMake will first tr
y
t
o
compile a s
a
mple
.
.
.
commit
|
commitdiff
|
tree
2010-10-29
Ros
s
en Ap
o
s
tolo
v
added g
_
kinet
i
cs to the CMake
b
uild sc
r
i
pts
commit
|
commitdiff
|
tree
2010-09-25
R
o
s
sen
A
post
o
lov
R
e
verted changes to md_openmm
.
c, get rid of 'nan' in
.
.
.
commit
|
commitdiff
|
tree
2010-09-25
Ross
e
n A
p
ostol
o
v
mdrun-g
p
u now doe
s
n't output indi
v
idua
l
energy t
e
rm
.
.
.
commit
|
commitdiff
|
tree
2010-09-21
R
ossen Apostolo
v
F
i
xe
d
missing ins
t
allation of the
openmm_api_
w
rapper
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
R
o
s
s
en Apostolov
A
d
d
e
d
do
_
multiprot in
src/contr
i
b, thanks to Ran Friedman
commit
|
commitdiff
|
tree
2010-09-13
Rosse
n
Apostol
o
v
Added
d
ependencies fo
r
o
penmm_api_wrapper
commit
|
commitdiff
|
tree
2010-09-13
Rossen Apo
s
tolov
A
dded lib
r
ary depen
d
e
n
cy fo
r
gmx_gpu_utils
commit
|
commitdiff
|
tree
2010-09-07
Ro
s
s
en
Apos
t
olov
M
erge branch
'
release-4
-
5-patches'
commit
|
commitdiff
|
tree
2010-09-06
R
ossen Apostolov
A
d
ded a note that running in d
o
uble precisi
o
n is sl
o
wer
.
commit
|
commitdiff
|
tree
2010-09-06
R
ossen
Apostolov
A lot of
C
M
ake optio
n
s are
n
ow
marked as adv
a
nced
s
ince
.
.
.
commit
|
commitdiff
|
tree
2010-09-02
Rossen
A
p
o
stolov
An
o
ther missi
n
g CMake
file
.
commit
|
commitdiff
|
tree
2010-09-02
Rossen Apos
t
olov
Merge bran
c
h 're
l
ease-4-5-patches'
commit
|
commitdiff
|
tree
2010-09-02
Ro
s
s
en Aposto
l
o
v
U
p
dated the version n
u
mbers t
o
4
.
5
.
1
.
commit
|
commitdiff
|
tree
2010-09-02
Rossen Apostolov
Added for
d
i
s
tribution missi
n
g CM
a
ke specific files
.
commit
|
commitdiff
|
tree
2010-09-01
Rossen Apostol
o
v
N
ew re
l
ease: 4
.
5 (final)
.
Yay!!
!
commit
|
commitdiff
|
tree
2010-09-01
Rossen
Apostolov
Added g_r
m
s
d
ist and
g
_rotmat to the
C
Ma
k
e build sys
t
em
commit
|
commitdiff
|
tree
2010-09-01
Rossen
A
postolov
Sm
a
ll
u
pdate of the GPU related docum
e
ntation
.
commit
|
commitdiff
|
tree
2010-09-01
R
o
s
s
en Apos
t
olov
Small update of the GPU relate
d
documenta
t
io
n
.
commit
|
commitdiff
|
tree
2010-09-01
Ro
s
se
n
Apostolov
Merge branch
'release-4-5-p
a
t
c
hes' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Ros
s
en Apostolov
Me
r
g
e
bra
n
c
h 'release-4
-
5-patches'
o
f git
.
gro
m
acs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Ros
s
en A
p
ostolov
Merge branch 'release-4-5-pa
t
ches' of git
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Ross
e
n Apostolo
v
OpenMM
now acce
p
ts cut-off method, s
i
nce it's nee
d
ed
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Ros
s
en Aposto
l
ov
New rele
a
se 4
.
5-
b
eta4
commit
|
commitdiff
|
tree
next