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Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
2010-10-28
Davi
d
van der
S
p
o
el
Merge
br
a
nch 'release-4-
5
-patches
'
of git
.
gr
o
macs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-08
David va
n
der S
p
oel
Me
r
g
e
branch 'release-4-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-09-28
David
v
an der S
p
o
el
Re-a
d
ded g_kineti
c
s to src/tools/Makefile
.
am
commit
|
commitdiff
|
tree
2010-09-24
David
v
an der
S
poel
Upda
t
ed
t
o r
e
flec
t
bug 557
.
commit
|
commitdiff
|
tree
2010-09-16
D
a
vi
d
van der Spoel
Corrected name of one of the developers l
i
sted in header
.
commit
|
commitdiff
|
tree
2010-09-14
David v
a
n de
r
Spoel
Fixed bug 553 by checking whether an atom nam
e
i
s
longer
.
.
.
commit
|
commitdiff
|
tree
2010-09-12
David van der Spoel
Fixe
d
demo to
w
ork with new pdb2gmx t
h
at
req
u
ire
s
two
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
David
v
an der Spoel
M
a
d
e
genr
e
str
-
constr t
o
produ
c
e constraints
of
ty
p
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
D
avi
d
va
n
der Spoel
Fi
x
ed bug 417
.
commit
|
commitdiff
|
tree
2010-08-19
D
a
vid van der Spoel
Fi
x
es
m
ore miser
y
in functi
o
n skip
s
tr
,
w
h
e
re pointers
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
David van der Spoel
Ad
d
e
d
two
m
issing
i
nc
l
u
d
e
file
s
.
Fi
x
ed ho
r
rible coding
.
.
.
commit
|
commitdiff
|
tree
2010-08-04
David va
n
der Spoel
Fixed
r
euse
of var
i
able
as
temp variable before p
r
i
n
ting
.
.
.
commit
|
commitdiff
|
tree
2010-08-03
David van der S
p
oel
F
ixed
bug 487 accordi
n
g to prov
i
ded p
a
tch
.
commit
|
commitdiff
|
tree
2010-08-03
D
a
vid
v
a
n
d
er Spoel
Fixed d
o
cumen
t
ation text accord
i
ng
t
o bug
z
illa 486
commit
|
commitdiff
|
tree
2010-08-01
D
avid van d
e
r Spoe
l
Merge branch 'release-4-5-patc
h
e
s
' o
f
g
i
t
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-01
David van de
r
Spoel
Moved pdb2top
.
h from sr
c
/kernel to include to allow
.
.
.
commit
|
commitdiff
|
tree
2010-07-31
David
v
a
n der Spoel
Rena
m
ed typename
to my_t
y
penam
e
in
index
.
c since
typename
.
.
.
commit
|
commitdiff
|
tree
2010-07-15
D
a
vid van der Sp
o
e
l
Fixed compilat
i
on iss
u
e
corresponding to bug 4
6
8
commit
|
commitdiff
|
tree
2010-07-13
D
a
v
i
d van der Spoel
Fixed bug
4
6
6 by commen
t
ing out
t
he of
f
ending lines
.
.
.
commit
|
commitdiff
|
tree
2010-07-08
David van d
e
r Spo
e
l
Merge branch
'
m
a
ster' of git
.
grom
a
cs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-07-08
David
v
an der Spoel
Ad
d
ed bonde
d
ty
p
es section
to rtp files
.
It might be
.
.
.
commit
|
commitdiff
|
tree
2010-07-03
Da
v
id va
n
der Spoel
Fixed
in
c
l
u
d
e statements su
c
h
t
hat double
p
r
ecision
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
D
a
v
id van der Spoel
M
e
rg
e
bran
c
h 'master'
o
f git
.
gromacs
.
o
rg:gr
o
m
acs
commit
|
commitdiff
|
tree
2010-07-02
David van der
S
p
oel
M
a
d
e
removin
g
pbc non-static
.
Thi
s
af
f
ects m
a
ny
a
n
a
lysis
.
.
.
commit
|
commitdiff
|
tree
2010-07-02
Davi
d
van der
Spoel
M
e
r
g
e
branch 'master'
of
git
.
gromacs
.
org:grom
a
c
s
commit
|
commitdiff
|
tree
2010-07-02
David van
d
er Spoel
Fixed
b
ug http://
b
ugzil
l
a
.
gromacs
.
org/show_bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
David v
a
n der Spoe
l
Fixed http://bugzilla
.
gromacs
.
org/show
_
bug
.
cgi?id=45
7
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
Da
v
id van der Spoel
Merge branch 'master
'
of git
.
gro
m
a
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-30
Dav
i
d van der S
p
oel
F
ixed bug in b-factors output by g_confrms
.
They were
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
D
avi
d
van der
Sp
o
el
Added mi
s
sing argument step
t
o
t
rott
e
r_up
d
a
t
e
.
How
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
David van der S
p
oel
Merge branch
'
m
a
s
ter' of git
.
gro
m
acs
.
org:
g
ro
m
ac
s
commit
|
commitdiff
|
tree
2010-06-27
D
avid v
a
n de
r
S
poel
Updated
CMakeLists
.
txt i
n
ngm
x
director
y
to exclude
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Da
v
id van d
e
r
S
poel
Fixed many
is
s
ues
r
e
g
ard
i
ng to compilation w
i
t
h C+
.
.
.
commit
|
commitdiff
|
tree
2010-06-18
David van der Sp
o
el
F
ixed Makefil
e
.
a
m
l
e
ading to w
a
rnin
g
s
.
commit
|
commitdiff
|
tree
2010-06-14
David van der Spoel
Fi
x
ed ma
k
e_edi
.
c
commit
|
commitdiff
|
tree
2010-06-14
D
a
v
id van der Spoe
l
M
e
rge branch 'maste
r
'
o
f gi
t
.
gromacs
.
org:g
r
omac
s
commit
|
commitdiff
|
tree
2010-06-14
David van
d
er Spo
e
l
Added mo
r
e fixes
i
n comment t
e
xts, generously
pro
v
ide
d
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
Davi
d
van der
S
po
e
l
Fixed a
lot
of spe
l
l
i
ng errors in comments and doc
u
mentation
.
.
.
commit
|
commitdiff
|
tree
2010-06-11
D
a
vid van der Sp
o
el
Mer
g
e branch '
m
aste
r
' of git
.
gromacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2010-06-11
D
av
i
d van d
e
r
Spo
e
l
Fix
e
d for
c
e fie
l
d
files f
o
r ATP i
n
order to clear b
u
g
commit
|
commitdiff
|
tree
2010-06-10
David va
n
de
r
Spoel
M
erge
b
ranch 'master' of git
.
gromac
s
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2010-06-10
David van
d
er
S
p
o
el
M
ade legend more or l
e
ss work i
n
g_ch
i
.
Don't
k
n
ow
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David
van
der S
p
oel
Fixed SEGV in g_ch
i
a
s
descri
b
ed in bug 430
.
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
van der
S
poel
Added option -nopbc
t
o
g_rmsdist in order to fix
commit
|
commitdiff
|
tree
2010-06-10
D
a
v
id van der Spoel
Pedantic change
in th
e
check
w
h
ether a fi
l
e
n
a
me is
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van
der Spo
e
l
Renamed some pr
o
g
r
ams to
follow the
g
_ doctrine: luck
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
David van
d
e
r S
p
oel
Clea
n
e
d
up and renamed files in ngmx direc
t
or
y
t
o
better
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Davi
d
v
a
n de
r
Spoel
Renamed som
e
files in a roundabout way to ad
h
ere
to
.
.
.
commit
|
commitdiff
|
tree
2010-06-10
Dav
i
d
v
a
n d
e
r
S
po
e
l
Rem
o
ved average
.
c
,
that function
a
l
ity
i
s now in g_
a
nalyze
.
commit
|
commitdiff
|
tree
2010-06-10
Dav
i
d
v
an der Spo
e
l
Fixed strange typo in gmx_dih
.
c
commit
|
commitdiff
|
tree
2010-06-06
David van der S
p
oel
Moved warning me
s
sage in
add
_
atomtype t
o
be prin
t
ed
.
.
.
commit
|
commitdiff
|
tree
2010-06-03
Dav
i
d v
a
n der Spoel
M
a
de
x2
t
op
(
v
e
ry) slig
h
tly f
u
nctional ag
a
i
n
.
Still
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der
S
poe
l
Cha
n
g
ed err
o
r message fo
r
settle pr
o
blems, such that
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
D
a
vi
d
van der
Spoel
Added
explicit angle in
ACE declaration in gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
David van der Spoe
l
Fixe
d
type i
n
gm
x
_morph
.
c:
efTRO
-
> efTRX which lead
.
.
.
commit
|
commitdiff
|
tree
2010-06-02
Da
v
id va
n
der Spoel
Fixed
b
u
g
3
9
6
.
In fact it was alre
a
dy
f
i
xed partly
.
commit
|
commitdiff
|
tree
2010-05-25
David van der
Spoel
Merge br
a
nch
'
master' of git
.
gromac
s
.
org:gromacs
commit
|
commitdiff
|
tree
2010-05-25
D
avid van d
e
r
Spoel
Added one
more!
commit
|
commitdiff
|
tree
2010-05-21
Dav
i
d van de
r
Spoel
Fixed compilation w
a
r
nin
g
s an
d
removed spur
i
ous C+
.
.
.
commit
|
commitdiff
|
tree
2010-05-20
D
a
v
i
d van der Sp
o
e
l
Made g_an
a
lyze
c
o
mpile again, but ot
l
in
k
yet
.
commit
|
commitdiff
|
tree
2010-05-19
David van der Spoel
Merge b
r
anch 'ma
s
ter
'
o
f
git
.
gromacs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-05-19
David van
der Sp
o
el
Added check i
n
read_pdb f
o
r existen
c
e
o
f t_res
i
n
f
o
.
.
.
commit
|
commitdiff
|
tree
2010-05-18
D
avid van der Spoel
Ad
d
ed a
cool
qu
o
te, a
n
d removed two comma's in openmp
.
.
.
commit
|
commitdiff
|
tree
2010-05-16
David van der Spoel
Merge
b
ranch 'master' of
git
.
gromacs
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-05-16
D
avid van d
e
r
Spoel
Fixed
sc
a
t
t
ering
f
unc
t
ion code
i
n g
_
rdf
.
A new f
i
le
.
.
.
commit
|
commitdiff
|
tree
2010-04-30
David van d
e
r Spoe
l
Added one
commit
|
commitdiff
|
tree
2010-04-04
David
v
an der Sp
o
el
Added
one
.
commit
|
commitdiff
|
tree
2010-04-04
David van der Spoel
Merge
branch 'master' of git
.
gromacs
.
o
r
g
:gr
o
macs
commit
|
commitdiff
|
tree
2010-03-12
David van der Spoel
M
e
rge branch 'mas
t
e
r
' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-03-12
David van der Spoe
l
A
dded flu
s
h
aft
e
r
writin
g
to debug file
commit
|
commitdiff
|
tree
2010-02-14
D
avid van
der Spoel
Added
f
unc
t
ion
to
i
n
cr
e
a
s
e the array sizes in a t_atom
s
.
.
.
commit
|
commitdiff
|
tree
2010-02-13
David van der Spoel
Replaced some strcpy by strncpy to avoid overflows
.
commit
|
commitdiff
|
tree
2010-02-06
Davi
d
van der
S
poel
Re
p
laced t
w
o
s
trcpy
by strnc
p
y in pd
b
io
.
c to prevent
.
.
.
commit
|
commitdiff
|
tree
2009-12-14
D
a
vid
van
d
er
Spoel
Cha
n
ged atom
n
umbe
r
f
o
r
O
S (opl
s
_
1
79,
o
pls_180) to
8
.
.
.
commit
|
commitdiff
|
tree
2009-12-07
Dav
i
d van der
Spoel
Merge
branch
'
master'
of git
.
g
romacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2009-12-07
David
v
an der
Sp
o
el
Updated
commit
|
commitdiff
|
tree
2009-12-01
Dav
i
d van der S
p
o
el
Adde
d
inclu
d
e/vmdio
.
h to the installable headers due
.
.
.
commit
|
commitdiff
|
tree
2009-11-15
David van
der Spoe
l
A
dded
c
h
e
ck for chdir r
e
turn value
.
commit
|
commitdiff
|
tree
2009-11-10
David van der S
p
oe
l
Ad
d
ed 2!!!
commit
|
commitdiff
|
tree
2009-09-18
D
a
vid van
d
er Spoe
l
Added
a
l
o
t
o
f help te
x
t
commit
|
commitdiff
|
tree
2009-09-18
David va
n
der Spoel
Rem
o
ved c
o
n
fusing -
-
disabl
e
-ni
c
e
commit
|
commitdiff
|
tree
2009-09-18
Davi
d
van der
S
poel
Mer
g
e branch '
m
as
t
e
r' of
gi
t
.
g
romacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-09-18
Da
v
id van der S
p
o
e
l
Adde
d
functi
o
na
l
ity to cha
n
ge d
i
re
c
t
o
rie
s
and ba
c
k
.
.
.
commit
|
commitdiff
|
tree
2009-09-18
D
a
v
i
d van d
e
r S
p
oel
Fixed compilat
i
on issue
.
commit
|
commitdiff
|
tree
2009-09-15
David
va
n
d
e
r
S
poel
Mad
e
reg
u
lar histogram
f
or g_clust
i
ze
t
o
r
eprese
n
t
.
.
.
commit
|
commitdiff
|
tree
2009-09-14
D
a
vid
van der Spoel
M
e
rg
e
branch 'master'
o
f git
.
groma
c
s
.
org:
g
romacs
commit
|
commitdiff
|
tree
2009-09-14
D
a
vid
v
an der Spo
e
l
Made statistics work with only 1
d
ata point
commit
|
commitdiff
|
tree
2009-08-27
David va
n
der Spoel
Merge bran
c
h 'master' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-08-27
Dav
i
d va
n
de
r
Spoel
Made
thread stuf
f
opt
i
onal
commit
|
commitdiff
|
tree
2009-08-27
Da
v
i
d
van der Spoel
Added
m
i
s
sing filename
commit
|
commitdiff
|
tree
2009-08-26
David van d
e
r Spoel
Made co
m
pilable agai
n
commit
|
commitdiff
|
tree
2009-07-19
David
v
an d
e
r Spoel
R
e
moved do
u
bles
commit
|
commitdiff
|
tree
2009-07-10
D
avid van der Spoel
Merge bra
n
ch '
m
a
ster' of
git@git
.
gromacs
.
o
rg:gromacs
commit
|
commitdiff
|
tree
2009-07-10
David
van der Spoel
Fi
x
e
d
erroneous
chec
k
s for
N
ULL
pointers
.
commit
|
commitdiff
|
tree